I was robbed last weekend of about 4.7 BTC's. My bitcoin client was corrupted when I opened it after a weekend away and would not sync. After repeated efforts to re install it it still would not sync. Finally I was able to install a new version on a different user on my computer and download the entire blockchain again and then open my backup.dat only to find a 0.00 balance. I'm done with bitcoin.
A wallet can have multiple addresses in it, and all of the coins aren't necessarily stored in your main bitcoin address. When you send coins, it will sometimes send the remainder back to you at a new hidden address that is stored in your wallet but not shown in the client. If you still have a backup of your old wallet.dat, there are ways to recover it. If you want some help, I can show you what you need to do to check it out.