I'm also having issues (probably related) with the latest Java3d (1.6.0-pre7). Here's a screenshot:
The basic layout here is that the various visualizations are shown in a tabbed pane. When I choose the tab for the 3D display it displays as in the screenshot rather than in the tab panel. It also always stays at the front, even when other tabs are selected. The content is correct though and updates nicely as the simulation runs. This all worked fine before with jogl 1.1.1 the original Java3D and java < 7. I'm assuming this java3D problem is caused by the jogl related issues but wanted to make sure.