First of all, are you on linux or windows?
Try repair into the console. Just be sure you keep a backup of your wallet.dat and you will be ok.
Edit: DO NOT USE CRYPTSY, THEY DONT TAKE THE TIME TO FIX THE WALLET AND ARE NOT ON THE GOOD CHAIN.
I'm using a windows and i had a backup of the whole old folder from the prevous version of the wallet where the coins still are but it is not updating the blockchain. Removing the blockchain files did made it update but the coins ware gone. It took some time so i'm going to try to get the privete keys out and put them back together now.
Edit: Now i'm waiting for the bootstrap.dat file to load. I think that it is going to work.