That can get highly irritating. I had 2 spots on a camera I had till recently, and just a couple of rocket blower uses completely cleaned it. Hope someone here knows of a way to get your problem fixed as well.
I have this issue with my III as well, and it's NOT on the focus screen. It's higher up near the prism and I've only been able to get it off when sending it into canon. For some reason my III is just an endless dust collector.
I had a problem like this when I used a homemade lens (don't ask). I literally had to use a turkey baster to force the sucker out of my camera's insides. It was soo annoying!