It may be the focusing screen. Mine constantly gets lint and dust on it no matter how much I try to clean it. When you take the lens off and look at the mirror, what you're looking at is the focusing screen. Try cleaning it with a blower, it may help
Put on two different lenses. If it's there with both, then it's not in the lens, it's in the voewfinder and it won't affect the image at all. Might be a nagging pain looking at it all the time but I got used to mine.
I had the same thing with my 400D - it ended up its on the inside of the camera on the glass below the viewfinder above the mirror. Most got in there when I cleaned the mirror thinking thats where the original mark i had was. Blowing it with some air cleaned most of it off but i've still got a little bit of stuff on there.