You checked the sha256 sum of bitcoin-0.9.3-win64-setup.exe ?
If so, what sha256 sum your Bitcoin-qt.exe has. Just curious if the hosted file on bitcoin.org/en/download could be with malware at the time when you downloaded it...
I checked the timestamps on the file I downloaded and when the transaction took place. It appears that they were stolen a day prior to the upgrade. I just didn't see the transaction until I caught up with the blockchain.