Mini-stuttering in games

I've been running my custom system for about 10 months now, without any problems whatsoever. Games would run smoothly (primarily Starcraft II, Dota II, Counter Strike: Source). Recently, I had to transport my desktop, and in the transportation process, the bag my desktop was in got shaken up some and my PC wouldn't boot. I then disassembled and breadboarded and got it working again before I put it back in the case. Now, my machine seems to run fine, but when I try to play games I get a very short stutter every few seconds when playing. It lasts only milliseconds (yet happens every few seconds), but it's really frustrating. I wonder if I damaged something when trying to put everything back in the case.

My laptop used to have a worse stuttering problem, but I believe it was due to overheating in that case. Here on my PC however, HWINFO and Speccy both report temps that seem fine. My CPU is about 60-70C max, and GPU seems to be around 50-65C (I think these temps are fine). I don't think that points to overheating. When I opened the side of my case, I touched the video card and it seemed to be hot (as expected), but the temps don't lie, so I guess that rules out overheating (correct me if I'm wrong). I don't think frames are a problem at all.

I'm not sure if there's an issue with the video card, CPU, motherboard or RAM. I ran the Win7 builtin memory diagnostic and seems that everything is fine with the memory. I get this lag even when I set SC2 on the lowest settings (I am normally able to run it with no problem at all on High/Ultra). All drivers are the same as they were 3 days ago, when all my games were running great, so I doubt that's an issue.

Could you guys please offer some advice as to what might be the issue here?

My specs are as follows:

AMD 965 Black 3.4ghz CPU
Asus M5A88-V EVO Mobo
Samsung Spinpoint F3 1TB 7200rpm HDD
Samsung MZ-7PC064D/AM 60GB SSD
OCZ 600MXSP 600w PSU
12gb PNY XLR8 1600mhz RAM
XFX Radeon 6870HD GPU

Thanks in advance,
-ns