Hello again,
I investigated a bit further, was trying to reproduce the error.
If I double-click on the original shellscript with nautilus and choose "run" it will crash when it reaches the menu (nothing changed at all).
http://pastebin.com/MHtHdYXzIf I do the same with my modified shellscript, it runs (seemingly) correctly, but also produces a hs_err_pid*.log file after quitting.
http://pastebin.com/FnDjsyZNSame happens if you use a launcher.
I didn't notice that it generated error files, there was 1 for every start of the program.

Starting starfarer from the terminal (or choosing "run in terminal" in nautilus) will run the game without crashes at all. weird.
The downside from running in terminal: If you have visual effects enabled it will flicker like ****. Seizure warning.
I think the flickering is a problem related to fglrx, I've also encountered it on some other games using lwjgl (Minecraft and every game from puppy games) and also some other opengl games.
I haven't tried using the sun (oracle :/ ) jvm. Don't want the "partners" ppa.
