Ensure the user library directory is empty.
Drop a container, say AnchorPane, then one asset on it, say a Button.
From Hierarchy initiate a drag of the Button and drop it to the Library: a Custom section appears that contains button_1.

Now open another SceneBuilder window ==> the Library panel is empty.
Click in this empty panel and you get:

dhcp-grenoble-10-166-105-112:MacOS yjoan$ ./JavaFX\ Scene\ Builder\ 2.0
Exception in thread "JavaFX Application Thread" java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
at java.util.ArrayList.rangeCheck(ArrayList.java:638)
at java.util.ArrayList.get(ArrayList.java:414)
at com.sun.javafx.collections.ObservableListWrapper.get(ObservableListWrapper.java:87)
at com.sun.javafx.scene.control.behavior.AccordionBehavior$AccordionFocusModel$1.changed(AccordionBehavior.java:170)
at com.sun.javafx.scene.control.behavior.AccordionBehavior$AccordionFocusModel$1.changed(AccordionBehavior.java:160)
at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:347)
at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
at javafx.beans.property.ReadOnlyBooleanPropertyBase.fireValueChangedEvent(ReadOnlyBooleanPropertyBase.java:72)
at javafx.scene.Node$FocusedProperty.notifyListeners(Node.java:7486)
at javafx.scene.Scene$15.invalidated(Scene.java:2076)
at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:111)
at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:145)
at javafx.scene.Scene$KeyHandler.setFocusOwner(Scene.java:3910)
at javafx.scene.Scene$KeyHandler.requestFocus(Scene.java:3956)
at javafx.scene.Scene$KeyHandler.access$2200(Scene.java:3896)
at javafx.scene.Scene.requestFocus(Scene.java:2040)
at javafx.scene.Node.requestFocus(Node.java:7647)
at com.sun.javafx.scene.control.behavior.AccordionBehavior.mousePressed(AccordionBehavior.java:152)
at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:95)
at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:89)
at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
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.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$MouseHandler.process(Scene.java:3746)
at javafx.scene.Scene$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)