I have graphic glitches too with an ATI card.
I solve them underclocking a little bit the memory and core.
My card has 560/520 ... ireduce it to 550/510 and the problem "near" to disapears.
When the glitches apears, i simply press the "windows" key in my keyboard, and go for few seconds to my desktop, and when back to the sim, glitches goes off...
SH3 is the only game with this problem.