Start with a new document.
In Inspector set padding for the default AnchorPane to say 7, for one or several directions, it doesn't matter.
Set it again this time to 0: you get the stack below.

Exception in thread "JavaFX Application Thread" java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1749)
at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1632)
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.EventUtil.fireEventImpl(EventUtil.java:74)
at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
at javafx.event.Event.fireEvent(Event.java:204)
at javafx.scene.Node.fireEvent(Node.java:8175)
at javafx.scene.control.Button.fire(Button.java:185)
at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:182)
at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:96)
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.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$MouseHandler.process(Scene.java:3689)
at javafx.scene.Scene$MouseHandler.access$1800(Scene.java:3414)
at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1676)
at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2467)
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)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at sun.reflect.misc.Trampoline.invoke(MethodUtil.java:71)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at sun.reflect.misc.MethodUtil.invoke(MethodUtil.java:275)
at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1744)
... 75 more
Caused by: java.lang.AssertionError
at com.oracle.javafx.scenebuilder.kit.metadata.property.value.ComplexPropertyMetadata.updateFxomPropertyWithValue(ComplexPropertyMetadata.java:70)
at com.oracle.javafx.scenebuilder.kit.metadata.property.value.SingleValuePropertyMetadata.setValue(SingleValuePropertyMetadata.java:108)
at com.oracle.javafx.scenebuilder.kit.metadata.property.value.SingleValuePropertyMetadata.setValueObject(SingleValuePropertyMetadata.java:139)
at com.oracle.javafx.scenebuilder.kit.editor.job.ModifyObjectJob.redo(ModifyObjectJob.java:87)
at com.oracle.javafx.scenebuilder.kit.editor.job.ModifyObjectJob.execute(ModifyObjectJob.java:74)
at com.oracle.javafx.scenebuilder.kit.editor.job.ModifySelectionJob.execute(ModifySelectionJob.java:79)
at com.oracle.javafx.scenebuilder.kit.editor.JobManager.executeJob(JobManager.java:174)
at com.oracle.javafx.scenebuilder.kit.editor.JobManager.push(JobManager.java:66)
at com.oracle.javafx.scenebuilder.kit.editor.panel.inspector.InspectorPanelController.pushJob(InspectorPanelController.java:1125)
at com.oracle.javafx.scenebuilder.kit.editor.panel.inspector.InspectorPanelController.setSelectedFXOMInstances(InspectorPanelController.java:1115)
at com.oracle.javafx.scenebuilder.kit.editor.panel.inspector.InspectorPanelController.updateValueInModel(InspectorPanelController.java:1044)
at com.oracle.javafx.scenebuilder.kit.editor.panel.inspector.InspectorPanelController.access$600(InspectorPanelController.java:139)
at com.oracle.javafx.scenebuilder.kit.editor.panel.inspector.InspectorPanelController$4.changed(InspectorPanelController.java:1024)
at com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(ExpressionHelper.java:176)
at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80)
at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:105)
at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:112)
at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:145)
at javafx.beans.property.ObjectProperty.setValue(ObjectProperty.java:69)
at com.oracle.javafx.scenebuilder.kit.editor.panel.inspector.editors.PropertyEditor.userUpdateValueProperty(PropertyEditor.java:472)
at com.oracle.javafx.scenebuilder.kit.editor.panel.inspector.editors.InsetsEditor.linkValues(InsetsEditor.java:181)
at com.oracle.javafx.scenebuilder.kit.editor.panel.inspector.editors.InsetsEditor.linkValuesAction(InsetsEditor.java:166)
... 85 more