Hmm...tried that, even created a new account (only way to import a .dat file it seems) and it still ended up with the same numbers.
I noticed two of my transactions for buying humble bundles aren't showing up in blockchain, which should make blockchain's balance be higher if anything. Every other transaction is intact though.
Also tried looking at the pywallet.py --dumpwallet output and meticulously made sure all of the private keys with matching addresses are intact on blockchain...they're all there, not sure what could be missing. Even did the wallet debug thing and it found nothing missing.