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Hunting through the JavaFX issue reports, there are many rendering reports for the Rotate transforms.
I did however resolve MY issue with using a Scale Transform rather than a Rotate Transform. With my transparent canvas, they are visually equivilant. I'm sure I just shot myself in the foot playing with the "camera" angle, which seemed intuitive, but just didn't seem to get the job done.
Again, thaks to all who read and help here. What a great forum!!
The issue with your original rotate is likely that you are rotating with a zero z co-ordinate and using a ParallelCamera which clips along a near plane z=0 and a far plane of (approx) z = sceneheight (i.e. ParallelCamera is pretty much useless for any 3d work).
Likely if you switch to a PerspectiveCamera for the scene, the rotation will work (though in perspective now - which you may not have wanted). This is because PerspectiveCamera has a different set of clip panes, with a near plane clip at a negative z value.
At least those were some of the quirks of how these things work when I tested it a long time back.
The most likely related jira issue is: http://javafx-jira.kenai.com/browse/RT-15117 "Clipping doesn't work for objects in 3D"
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