Hmmmm. Look in your TB install location for stderr. It'll be somewhere, and it'll contain any errors that TB comes across including shader problems.
It won't be a clocked card issue - in *nix clocked/cooked cards produce little areas of coloured dots around the screen. Tis pretty. XD
One thing I can think of would be if an accelerated desktop was being used. Compiz used to produce bizarre lighting issues with some oGL games, so there's a possibility it could be the cause - providing it's being used of course.