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You could try to download the files again using different sources, then compare the files.
If I was you, I'd immediately disconnect the pc from the net (might got trojaned somehow), boot it up using a live cd (like ubuntu on cd or a usb stick) and copy my wallet out. Then I'd send all my coins to a new guaranteed unleaked wallet (like one created using the booted live cd).
Important: make a backup of the new wallet before you send any coins to it. Always make sure restoring your backup wallet works before deleting the old wallet.
About "you're not infected as your virus scanner doesn't find anything": that doesn't mean anything. Virus scanners hardly find trojans if they're not already known.
edit: How safe/long was your mtgox password? Can you tell it? You can't use it anymore anyways now.
Most important: did you use the same password somewhere else?