We do not have experience with JavaFX, so I cannot tell whether it is possible. It looks like Oracle withdraw from officially supporting embedded ARM (see this email).
It seems that JavaFX and its default renderer prism is written with hardware acceleration in mind. Note that Colibri VF61 does not come with a GPU, so you would have to run the renderer in software… Maybe this is the issue your are seeing? Can you try disabling the hardware renderer/force software rendering? This post shows how to force the software renderer:
I used software rendering forced with option “-Dprism.order=sw”, which is mentioned in your link, in all my cases - you can see my console outputs in attachments.
Vybrid uses DRM and the modesetting driver by default, which makes use of the hardware cursor. Maybe this causes problems for JavaFX. You can force X11 to use a software cursor by adding SWCursoron to /etc/X11/xorg.conf
Maybe using the fbdev instead of the modesetting driver helps? Otherwise, I have no idea… It would require deeper analysis, which we cannot do under support. Maybe the Java(FX) community can help, otherwise I would recommend to contact one of our software service partners.