The issue is dependable on jar and a way you start the tool.
So let's describe the worst case:
-clean user library folder
-start the tool from sources
-add attached jar
-move it to content panel
-move it from content panel back to library
following exception is thrown and vm has crashed

java.lang.AssertionError
    at com.oracle.javafx.scenebuilder.kit.metadata.util.DesignHierarchyMask.getSubComponentAtIndex(DesignHierarchyMask.java:555)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.driver.VBoxDriver.makeDropTarget(VBoxDriver.java:99)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.dragOverHitObject(DragGesture.java:317)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.dragOverGlassLayerBis(DragGesture.java:241)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.dragOverGlassLayer(DragGesture.java:221)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.dragEnteredGlassLayer(DragGesture.java:208)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.start(DragGesture.java:178)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.mode.EditModeController.activateGesture(EditModeController.java:980)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.mode.EditModeController.dragEnteredGlassLayer(EditModeController.java:910)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.mode.EditModeController.access$600(EditModeController.java:96)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.mode.EditModeController$7.handle(EditModeController.java:579)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.mode.EditModeController$7.handle(EditModeController.java:576)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:204)
    at javafx.scene.Scene$DnDGesture.handleExitEnter(Scene.java:3197)
    at javafx.scene.Scene$DnDGesture.processTargetEnterOver(Scene.java:3085)
    at javafx.scene.Scene$DnDGesture.access$6100(Scene.java:2896)
    at javafx.scene.Scene$DropTargetListener.dragEnter(Scene.java:2800)
    at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler$1.run(GlassSceneDnDEventHandler.java:59)
    at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler$1.run(GlassSceneDnDEventHandler.java:53)
    at java.security.AccessController.doPrivileged(Native Method)
    at com.sun.javafx.tk.quantum.GlassSceneDnDEventHandler.handleDragEnter(GlassSceneDnDEventHandler.java:53)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleDragEnter(GlassViewEventHandler.java:570)
    at com.sun.glass.ui.View.handleDragEnter(View.java:659)
    at com.sun.glass.ui.View.notifyDragEnter(View.java:981)
    at com.sun.glass.ui.win.WinDnDClipboard.push(Native Method)
    at com.sun.glass.ui.win.WinSystemClipboard.pushToSystem(WinSystemClipboard.java:234)
    at com.sun.glass.ui.SystemClipboard.flush(SystemClipboard.java:51)
    at com.sun.glass.ui.ClipboardAssistance.flush(ClipboardAssistance.java:59)
    at com.sun.javafx.tk.quantum.QuantumClipboard.flush(QuantumClipboard.java:274)
    at com.sun.javafx.tk.quantum.QuantumToolkit.startDrag(QuantumToolkit.java:1150)
    at javafx.scene.Scene$DnDGesture.dragDetectedProcessed(Scene.java:2940)
    at javafx.scene.Scene$DnDGesture.process(Scene.java:3009)
    at javafx.scene.Scene$DnDGesture.access$8400(Scene.java:2896)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3762)
    at javafx.scene.Scene$MouseHandler.access$1800(Scene.java:3471)
    at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1695)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2486)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:314)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:243)
    at java.security.AccessController.doPrivileged(Native Method)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:345)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:526)
    at com.sun.glass.ui.View.notifyMouse(View.java:898)
    at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
    at com.sun.glass.ui.win.WinApplication.access$300(WinApplication.java:39)
    at com.sun.glass.ui.win.WinApplication$4$1.run(WinApplication.java:112)
    at java.lang.Thread.run(Thread.java:744)

Exception in thread "JavaFX Application Thread" Error 80de0001 in CallbackToJava(javaIDs.View.notifyDragEnter, grfKeyState, pt ,pdwEffect )
COM Error: 80de0001 Unknown error 0x80DE0001

java.lang.AssertionError
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.performTermination(DragGesture.java:456)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.dragDoneOnGlassLayer(DragGesture.java:414)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture.access$500(DragGesture.java:75)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture$5.handle(DragGesture.java:155)
    at com.oracle.javafx.scenebuilder.kit.editor.panel.content.gesture.DragGesture$5.handle(DragGesture.java:151)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
#
# A fatal error has been detected by the Java Runtime Environment:
#
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
# EXCEPTION_UNCAUGHT_CXX_EXCEPTION (0xe06d7363) at pc=0x75a1c41f, pid=12872, tid=19960
#
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
# JRE version: Java(TM) SE Runtime Environment (8.0-b132) (build 1.8.0-b132)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
# Java VM: Java HotSpot(TM) Client VM (25.0-b70 mixed mode windows-x86 )
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
# Problematic frame:
# C [KERNELBASE.dll+0xc41f]
#
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
# Failed to write core dump. Minidumps are not enabled by default on client versions of Windows
#
# An error report file with more information is saved as:
# D:\work\authoring\2.0\scenebuilder\SceneBuilderApp\hs_err_pid12872.log
#
# If you would like to submit a bug report, please visit:
# http://bugreport.sun.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:204)
    at javafx.scene.Scene$DnDGesture.processDropEnd(Scene.java:3062)
    at javafx.scene.Scene$DnDGesture.access$6800(Scene.java:2896)
    at javafx.scene.Scene$DragSourceListener.dragDropEnd(Scene.java:3306)
    at com.sun.javafx.tk.quantum.GlassScene$3$1.run(GlassScene.java:252)
    at com.sun.javafx.tk.quantum.GlassScene$3$1.run(GlassScene.java:247)
    at java.security.AccessController.doPrivileged(Native Method)
    at com.sun.javafx.tk.quantum.GlassScene$3.actionPerformed(GlassScene.java:247)
    at com.sun.glass.ui.Clipboard.actionPerformed(Clipboard.java:173)
    at com.sun.glass.ui.win.WinDnDClipboard.push(Native Method)
    at com.sun.glass.ui.win.WinSystemClipboard.pushToSystem(WinSystemClipboard.java:234)
    at com.sun.glass.ui.SystemClipboard.flush(SystemClipboard.java:51)
    at com.sun.glass.ui.ClipboardAssistance.flush(ClipboardAssistance.java:59)
    at com.sun.javafx.tk.quantum.QuantumClipboard.flush(QuantumClipboard.java:274)
    at com.sun.javafx.tk.quantum.QuantumToolkit.startDrag(QuantumToolkit.java:1150)
    at javafx.scene.Scene$DnDGesture.dragDetectedProcessed(Scene.java:2940)
    at javafx.scene.Scene$DnDGesture.process(Scene.java:3009)
    at javafx.scene.Scene$DnDGesture.access$8400(Scene.java:2896)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3762)
    at javafx.scene.Scene$MouseHandler.access$1800(Scene.java:3471)
    at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1695)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2486)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:314)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:243)
    at java.security.AccessController.doPrivileged(Native Method)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:345)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:526)
    at com.sun.glass.ui.View.notifyMouse(View.java:898)
    at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
    at com.sun.glass.ui.win.WinApplication.access$300(WinApplication.java:39)
    at com.sun.glass.ui.win.WinApplication$4$1.run(WinApplication.java:112)
    at java.lang.Thread.run(Thread.java:744)
Exception in thread "JavaFX Application Thread" Error: 80de0001 in checkJavaException(env)