Are there a bunch of flashing lights on the screen or anything? Is it possible for you to play without your glasses on? It might not be bad, but it's something you need to get checked out if it continues.
I've personally never played Guitar Hero, but I know that when I'm riding a train and staring out the window at the ground for a while, and the train stops, I've still got the illusion of the ground moving away from me. This wears off after a couple of seconds. I don't think it's anything to be concerned about, don't know if your case is similar.
I think its because I am staring at a fixed place on screen while it has a constantly moving background...however my 360 just broke today the day I get game....so now In a way GH2 is gonna cost me $240 to play with repair costs.
I'd see a doctor... I guess the acid trips are included with GH2! lol
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It's more of a brain than a vision thing. You could compare it to what your eyes do when you spin around really fast about 10 times and get dizzy. I got kind of tired of it so I learned to play most songs without looking at the screen too much.