You said someone withdrew from your "account". What wallet were you using?
standard bitcoin client with 12 digit password
Well if you resused the password then you can assume it was compromised somewhere. Expensive lesson but never reuse passwords for anything financial related. If you want to be lazy and reuse the same password for steam games and twitter that is one thing but anything financial related should be unique.
You indicated your system came back clean so:
1) Do you have a backup of your wallet.dat? Is the backup stored online? Have you emailed the backup to yourself?
2) Does anyone else have physical access to your computer?