Well, I admit that it does the same with my saved games... so I do the cheesy trick: I backup the save games (as I usually do) to another folder (removing them from the original one - cut->paste) and leave only the ones I want scanned. That seriously decreases the waiting time.
After I'm done, I restore the saved games. It's all about bunch of cut/copy and paste tricks and it saves quite some time - keeping in mind that the scanner also checks the quicksaves...
