You say Windows can find trs, do you mean can't?
What sort of windows reinstall-complete wipe or just let it reinstall over itself (which often doesn't clear out problems....)?
I would think you will have to reinstall TRS and then the patch otherwise the windows registry won't clock where it is and CMP etc may not function?
You could try renaming your original installation directory, then reinstalling just the 2006 prog, then copy back over from your old directories?