In the attached test is a group of Custom nodes (ShapeGrid) added to a HBoxVBox layout as follows:
        var mainGroup:VBox = VBox {
            id: "Vbox-Hbox"
            spacing: bind vertSpacing.value
            content: bind [for (i in [1..6])
                HBox {
                spacing: bind horizSpacing.value
                content: bind [for (i in [1..6])
                    ShapeGrid {
                                 ....
                }
                ]
            }
            ]
            .....
            visible: bind visibleBox.selected
        }

1) Run the test and un check the visible checkbox to make the Node invisible.
2)Now change the various attribs such as rotation, opacity VertSpacing, etc.
3) Click on visible - The Nodes are not visible. Change any of the attribs again and it appears back.
4)In case you do not see this right away repeat the above steps a few times and it is reproducible in 2-3 attempts.
4)Repeat the above steps - after a while the following exception thrown but it not consistently seen.

Unexpected exception caught in MasterTimer.timePulse():
java.lang.NullPointerException
at com.sun.scenario.scenegraph.SGFilter.render(SGFilter.java:266)
at com.sun.scenario.scenegraph.SGTransform.render(SGTransform.java:284)
at com.sun.scenario.scenegraph.SGWrapper.render(SGWrapper.java:123)
at com.sun.scenario.scenegraph.SGGroup.render(SGGroup.java:218)
at com.sun.scenario.scenegraph.SGGroup.render(SGGroup.java:218)
at com.sun.scenario.scenegraph.JSGPanel.paintComponent(JSGPanel.java:548)
at com.sun.javafx.scene.JSGPanelImpl.paintComponent(JSGPanelImpl.java:53)
at javax.swing.JComponent.paint(JComponent.java:1027)
at javax.swing.JComponent.paintToOffscreen(JComponent.java:5122)
at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:277)
at javax.swing.RepaintManager.paint(RepaintManager.java:1217)
at javax.swing.JComponent._paintImmediately(JComponent.java:5070)
at javax.swing.JComponent.paintImmediately(JComponent.java:4880)
at javax.swing.JComponent.paintImmediately(JComponent.java:4892)
at com.sun.scenario.scenegraph.JSGPanel.repaintDirtyRegions(JSGPanel.java:600)
at com.sun.scenario.scenegraph.JSGPanelRepainter.repaintAll(JSGPanelRepainter.java:106)
at com.sun.scenario.scenegraph.JSGPanelRepainter$FrameDisplay.run(JSGPanelRepainter.java:112)
at com.sun.scenario.animation.AbstractMasterTimer.timePulseImpl(AbstractMasterTimer.java:365)
at com.sun.scenario.animation.AbstractMasterTimer$MainLoop.run(AbstractMasterTimer.java:247)
at com.sun.embeddedswing.EmbeddedEventQueue.doPulse(EmbeddedEventQueue.java:440)
at com.sun.embeddedswing.EmbeddedEventQueue.access$000(EmbeddedEventQueue.java:70)
at com.sun.embeddedswing.EmbeddedEventQueue$2.run(EmbeddedEventQueue.java:347)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)