No, it might not be because of bad sectors, I'm sure of it. I had this similar problem. Each and every time I alt-tabbed out of the game, and went back in, the game runs at 5 FPS or so, and stutters for about 30 seconds. Then everything goes back to normal.
And after quitting the game, the stutter that you still experience, is most likely the problem with your CPU. As it may be getting a bit too worked up.
But PC specs are to listed anyways.