Firstly, I would re-run the verification without 'Keep unknown mods, make them inactive' checked. This will ensure that no additional mods are floating around other than the standard AAA set. Once that's done, use the Fix option to download the appropriate files to fill gaps/correct corrupted files. Once fixed, run the verify again to ensure no other problems are there. Assuming that there aren't, try launching the game. If the second verify does find anything wrong, run the Fix again. Once you get a clean Verify, you should be good to go. If you need a hand, I can make myself available on TS this afternoon. Send me a PM if I can do anything here to help you.
Jabo
P.S. Alternatively, uninstall the game completely (remove folders etc) and reinstall. Obviously you will have to reinstall the mods as well as remapping your keys, but if ChkMods doesn't solve the problem (and it should) this is the only option left open.