Question about how multiple hard drives affect computer operation

I'm thinking about reformatting my harddrive because a couple of games have been crashing and windows media player also crashed a few times. (I've tried everything else I can think of) But I have 2 hard drives hooked up. One has Windows and all of my programs on it. The other is a storage hd for documents, videos, etc.

My question is, could a virus or something on the storage hard drive be causing the problem even though Windows and my programs aren't installed on that drive? There's no way I'll reformat my storage drive but if that drive is the one with the problem then it would be pointless to reformat the other drive.

 

yes a virus could be in the "storage" drive