When I run OmegaT in Japanese, only the menus display correctly, source files dont display the right fonts. I've downloaded the older version (1.8) and everything there works just fine, so for now I'm going to use that one.
That's no real solution though, so I'm looking forward to hearing some other ideas.
You didn't answer my question:
Have you tried the new version with "Java included"?
Or maybe it's a bug that should be reported to the program developers?
As we do not have other reports, I doubt there's much we can do from within OmegaT (in case that's not obvious, I am one of the program developers). I recommend asking for help in the OmegaT Yahoo support group. There are more likely Ubuntu users in that group. You could try also the Linux for Translators group (also in Yahoo).