Yes, but Steam isn't 1.0 or 1.1. Its only steam and it isn't compatible with MTA or downloaded save games.
Downloaded save games why? Because they're for the normal Vice City and there are no patches for Steam. You have to start a new game.
That's your problem. The "virus" files stayed there. Therefore, the anti-virus doesn't detect them with no reason.
You must have to format your computer and then install Windows again.