Yeah, all the stuff under:
HKEY_CURRENT_USER\Software\JavaSoft\Prefs\com\fs\starfarer
I'd be shocked if that had anything to do with this issue, though, but can't hurt to try cleaning that up. Well, it
could hurt if you accidentally delete something else from the registry, so please do be very careful
The only thing that comes to mind is if you've possibly installed something/made some changes to your system between 0.6a and 0.6.1a. Hmm. If you updated your system's version of Java, it may be worth a shot replacing contents of the jre folder under
C:\Program Files (x86)\Fractal Softworks\Starsector
With the contents of the
C:\Program Files\Java\jreX (where 'X' is a number)
Or wherever it is that you've installed Java.