if you have not tried to restore the wallet yet you may find this useful:
I would seek the advice of some others before trying it , but if the btc is gone from that particular wallet i don't see how it can hurt anything.
In your case you would need to get what you are certain is a clean computer to run the bitcoin client on and I will describe how to rebuild your wallet,
1) Back up your entire folder that holds your wallet.. On windows find that in your directory
Users\name\AppData\Roaming\Bitcoin back it up in a safe place offline if possible
2) Start the qt wallet and export a log of all your present transactions and id's for safekeeping. From the transactions tab of the wallet click on file , export and save it in a safe place.
3) Click on Help, then debug window and finally the console tab to bring up the command line
4) On the command line type (no quotes) "listaddressgroupings" Copy and paste all the addresses to a text file. You can do them one at or time or all together. Save that text file but keep it open.
5) For each address (you may have only a few or several) type on the command line of your qt wallet (again no quotes)
'dumpprivkey' and a space then after paste in the address. The client will then give you a long set of letters and numbers. Copy and paste this with the address it matches up with in your text file to use later.
6) Repeat step 5 for each address that you have. You can copy each individually as you go or you can wait until finished and copy and paste the entire thing to a windows text file. Don't forget any. When finished save that text file in a safe place. If you copied the entire list at once windows may give you an error about saving special characters (should be safe to ignore).
7) Close the wallet. Delete anything in the Users\name\AppData\Roaming\BitCoin folder EXCEPT your conf file (unless you don't have one) and make sure you have everything backed up. (Not recommended to back up in this folder).
Make sure you have the most up to date version of the bitcoin client qt wallet installed.
9) Use the same method as in step 3 above to open the command line. Get that text file with the list of addresses and private keys and type on the command line (again no quotes) 'importprivkey' , a space, then paste a private key after it and hit enter. Wait a few seconds for the client to accept the command. Repeat as many times as necessary depending on how many private keys you had. Don't forget any. If you try to do one twice you should get an error.
10) Close your qt wallet up. It does not matter how much of the blockchain may have downloaded. Now let the entire blockchain download. Do not try any transactions just let it rolll.
11) When the blockchain is complete normally your coins would all be in there where they belong. If they were stolen by someone cloning your wallet and using these keys to steal them they will not be there.
12) Good practices: Never allow anyone to have access to your private keys. Keep the swap file disabled on any computer you use. If you own a large amount of bitcoin like this you should keep it in a secured (locked) wallet with a complex passcode which you can also encrypt and store off line
I saw a few other useful posts in this thread earlier for security in general. Most of it seemed like sound advice.
The method I described above is normally what would be used if you had lost coins from a paper wallet or if your wallet.dat file was corrupt for some reason and would not properly load or 'show' your coins. Just make sure that in this case you are performing this on an entirely clean system since you have not tracked down the method the thief used. I would even take the precaution to connect to the web to get the blockchain from a friends home or alternate source in case your local network is owned and the thief has control depending on your experience with these things.
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