Doing an un-install/re-install isn't your only option but its usually the easiest way.
I'm also running the SCX mod and I don't recall having problems with it.
You might want to check your SC install disc for scratches and smudges prior to doing a re-install. Otherwise, make sure you let the SCX install run completely once you verify that the stock game works. You should also download a fresh zip file for SCX here and install it.
Hang in there, sometimes these kinds of problems can be tricky to solve.