Don't take offense if I'm dumbing this down too far, just trying to edumacate ya!
If you get SH3D direct from the Download link, it includes it's own java that is known to work pretty reliably.
If you are installing SH3D from your distribution, they will strip out things that they think are wasteful. i.e. If every application includes their own java runtime, that's a lot of bloat. So in packaging the app for the distribution they strip out software components that they already have a version of, and make the component a dependency of the app.
Most of the time, this is fine. However Java + OpenGL + Gfx drivers on Linux seems to be quite fragile. Hence why in this particular case it would be better if distro packagers didn't faff around with the packaging. This tendency is why I only use the package provided on the SH3D site.
