It's my opinion that the stutters don't come from the HDD (maybe there are exceptions). I've tested the game on a HDD (7200) and on 3 very fast SSD's in a RAID 0 array (which is probably bottlenecked by the controller or bus). It's my experience that it makes totally no difference in stuttering. Thereby I have to say that my stutters are mostly mild.
I agree with TUSA/TX-Gunslinger that it has probably something to do with the code of the game. On the moments that you see a short heavy drop in FPS you see a simultaneous (more or less) drop in CPU utilization. Normally CPU utilization should increase when a game has lots to process.
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