Hi
I worked on a software (for Earth science) based on Eclipse RCP and "our" own visualizer (plain JOGL) several years ago.
You probably use SWT_AWT (the SWT/AWT bridge). I had to do some hacky things to make it work correctly with the debug pipeline. I'm a bit ill at ease because there is only one other high level 3D engine whose default renderer is based on JOGL and which doesn't require the use of a bridge for SWT integration but it isn't Java3D because there is no plan to add new features into it even though it is still actively maintained (big kudos to Harvey and some individuals of course). I fear that you'll have to go on using your clever workaround. Please share your findings (in details) and maybe I'll have something a bit smarter to suggest.