Desktop Stuttering

Hey everyone. Im not sure if this is the right category for this issue, so feel free to move me.

first off, here are my specs:

Intel Core 2 Quad Q6600 2.4ghz
eVGA nVidia 680i Mainboard
6GB of DDR2 RAM (2GB of Mushkin, 4GB of Corsair, cant remember the speeds)
nVidia 260 GTX Graphics
4 Seagate Barricuda HD's (two 7800.10's (80Gb and 500Gb) and two 7800.12's (500Gb and 1TB)
Corsair HX650 PSU
Windows 7 Ultimate Service Pack 1

note that all components are almost 4 years old except the 7800.12 drives, the graphics card, and the PSU (the card and PSU both failed on me last year, the drives are for expansion)

now my issue:

my computer stutters. it does so every second or so, and it affects audio, video, and actual response. everything freezes for about half a second. it does so at desktop, in 3D applications, even at the screensaver. if i continue to use the computer in this state, it will get worse and eventually freeze up completely, requiring a hard restart. (i hard restarted a few too many times last night and needed to use bootrec.exe to get it to boot again)

there are a few quirks about this:

firstly, it surfaced after i hadn't used the computer for over 2 months. i had been working out of town over the summer and kept the computer off. i come home, turn it on, and this happens.

secondly, if i let it idle for 30 minutes or so, SOMETIMES it will stop stuttering on its own. this is never permanent and it usually only lasts 15 min to an hour before it reverts to stuttering.

thirdly, 1/5 reboots will result in a stutter free desktop on boot. this can last for 1 hour to a whole day. two days ago i thought my problem was fixed spontaneously and used the thing for over 10 hours before it started stuttering and eventually froze.

it happens right at the login screen, before i actually log in to any account.

ive cleaned my registry, defragmented, updated my video driver, done a spyware and virus scan, and checked all my disks and RAM for consistency. nothing has turned up, except that small errors turn up almost every reboot on my programs disk (where i store and install all of my applications) but ill attribute that to hard booting the sucker too much.

any ideas?

EDIT: after re reading my post, it sounds like a heat problem. i really doubt this, as i have never had heat issues in the 4 years ive had this system. everything runs at a comfortable temp, even at load. ill dust out my case just to be sure

The first thing I would do is open your case up and blow it out. Get a can of dust off and make sure there is no dust inside of any of the heatsinks / fans.

As you said it does sound like a heat problem, but even though you haven't had any heat problems before letting it sit for a couple months can let dust settle and impead the performance of fans and airflow.

Also, remove and reseat GPU / RAM

Yes, Hopefully it was that easy

You are very welcome, glad it was that simple and you didn't need to replace anything

Note that its not nearly as bad as it was a few weeks ago. its definitely usable now.

maybe the original problem triggered after a windows update? i was gone for months, perhaps i had a backlog of stuff i unknowingly installed?