Did you try uninstalling the game completely, then re-install the game and patch before trying to run it?
Someone else had a problem where the game wouldn't start at all after re-installing Windows. Deleting the SecuROM User Data file and registry key (see their
FAQ) had it prompt for the serial code again, and the game loaded properly. Maybe that would help getting the updated version of the game to accept your serial?
Installing the wrong patch version can cause this problem, but that shouldn't be the case here if you went through Stardock's updater.
