Re: What the Fu**
The flies could've gone through the side fan which blows in. I can't think of any other ways for them to get in unless your case was open. All you other fans should be blowing out. Maybe your PC has neon lights or something and flies are attracted to it? You know, like those blue neon lights that restaurants uses to attract and electricute the flies.
*Fact: Microsoft Window's Blue Screen of Death vs Computerforums.org's White Screen of Death. Which is worse?