Ok, I've managed to figure out which file was causing the problem, or at least, I think I have.
The DS Romance mod comes with a sta_bastila.utc file, which I think mucks up the original one that is there for the command centre fight. Or at least, if I remove this file the command centre fight works fine (though admittedly the mod doesn't).
So I'm figuring that if that is the problem, then I can resolve it by renaming all references in the mod to that file and the file itself to something unique... But that might be my misguided and naive understanding of the way all this stuff is coded/scripted etc.