I guess you never read the forums and such a like, don`t worry though its not your system at all.
Amd sort of acknowledge a few days ago the Micro stutter on Ati 6990 card has a lot to do with the video drivers, they are working on a fix but have not come up with one yet.
The last driver they released had a back wards effect on frame rates btw knocking about 8fps to 10 off in some games. Its not just you loads of people have noticed, just hang in there till Ati fixes it with a new driver. Nvidia are also suffering the same problem driver related, same thing a bit of micro stutter in games.