PC Stutter Issues.

For some reason my 1 year old system is stuttering for some unknown reason. After it has been running for 30 minutes or so it starts to stutter on any function I do. Videos stutter like crazy, games stutter for a couple seconds then return to normal only to stutter again 30 seconds down the road. The system shouldn't be struggling because it is a fairly decent rig, I just can't seem to figure out what could be the problem.

Specs are
i7 920 processor
gtx 260
9gb ddr3
500gb hd
750w ps

Power supply, cpu throttling?

Check your temps when at full load with prime95 and hwmonitor or the like.

Now i've restarted and tried to run a CHKDSK and it's getting stuck at like stage 4 of 5 and when it says to press a key i mash on the keyboard haha and it won't skip it. My temps usually seem fine, CPU is 38. Sys 42. So now that problem has turned into something else, imagine that.

It ran for like 4 hours and stayed on the same number. About a week ago while i was playing a game the screen starting getting little squares all over it and buggin out so i quickly turned it off and every since then i've had this problem. SO i tried to run chkdsk just for the hell of it and now it's stuck there and i can't boot up wtf.

Ya is there anyway to bypass the chkdsk? I'd just like to boot it up.