Wallet.dat doesn't actually "contain" the coins, wallet.dat stores the private keys that own the coins. There are a few possibilities:
1. Wallet.dat was deleted and recreated (I don't know why this would happen). Corrupted maybe?
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2. You were hacked and they were stolen. In that case check your address(es) on blockchain.info
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3. They keys in your wallet were somehow lost (I don't know why this would happen either).
If you have the private keys they can be redeemed on Mt.Gox, Blockchain.info, or (I think) Armory.
EDIT: It looks like I misunderstood your post, and obviously #2 is not an option. Since I assume you didn't delete the Bitcoin folder in %AppData% (right?), the update must have overwritten it.
I hope I'm wrong!