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Computer Stutter/Lag/Freeze every few seconds

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I recently bought a new case, motherboard and ram. After installing a fresh copy of Windows 7, I noticed this weird type of lag. Every two seconds, my computer will freeze/lag/stutter(whatever you want to call it) for like not even a second. It didn't happen right at the beginning of switching my parts, but after a while it started, which was when I proceeded to installing another fresh copy of Windows 7, but it didn't fix the issue. I also noticed that my hard drive light on my case will glow at EXACTLY the same time as the stutter. I did not change my harddrive, so I don't think it could be a harddrive problem but I'm not too sure. This lag gets very annoying with anything in general, since it also makes my sound stutter which makes listening to music un-enjoyable, as well as gaming. My case comes with a lot more fans, and I'm using the same power supply so that might be the issue. Thank you for any help in advance.

Asus M5A97 MOBO
8GIG 1333 RAM
AMD 965 quad core
GTX 460 superclocked

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I am having the same problem as well. After I replaced my motherboard, I too have been having lag/stutter problems with my games, though not with music. I recently took my computer into the shop, though that hasn't resolved the issue either, and they came up with nothing to resolve the problem. I would really like to know what is wrong with my computer so I can fix it myself.

Current Specs:

Windows Vista
Intel Pentium Duo CPU 2.20Ghz
GeForce GTX 560Ti
ASUS P5QL-VM DO Motherboard
4 gigs of ram

Edit: And yes, I do believe all my SATA cables are plugged in correctly.

Any errors in the system log?
Sounds like a resource conflict from a driver issue or faulty hardware.

Try unplugging other devices until the stutter goes away, even PS2 keyboards/mice.

Moving peripherals from one USB port to another can change the behavior.

I've had my system lag from periodic reads of an external USB drive. The low power state causes a hiccup when the OS goes to check the status. During gaming it was bad enough that I just started turning it off.
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Where can I find the system log? Sorry, I'm not the most tech-savy when it comes to these sorts of things.

Also, I did as you suggested and unplugged all of the devices from my computer, and the stutter still persisted. Even when I plugged everything back into different ports, the stutter still remained. It can't be my graphics card, for I already purchased a new one [the GT560 TI] a few months back to see if that solved the issue [Of course, it didn't].

I know you said its a fresh copy of windows 7. But has it been doing it since the install? Or have you installed ANYTHING at all since? This has happened to me a couple times in a couple of different builds.. Background programs are almost always the case. ( IE. Windows Updates, Java updates, ANY kind of background updates.. ) Have you tried pulling all of the ram out and puting them back in 1 at a time to see if its ram? Did you put enough Thermal paste on? Is your computer overheating at all?? If none of that helps. I would like to think it is your Hardrive man.. Do you happen to have another hardrive to test it out?

I have the same problem on a windows7 64. Every two second the computer freezes for like almost 1 second.
When it starts it can take 20 mins or more before it goes away by itself. Of course i can reboot and it will go away.
Mostly it takes some hours before the problem begins, it does not show anything in eventviewer and no scheduled task started to run. Nothing unnormal in taskmanager.

I just now tried to end lots of processes one by one and see if it made any difference.
After ending these two it suddenly stopped freezing.
HsMgr.exe and HsMgr64.exe.
I will try it next time it happens so I know for sure, it may also have been a coincidence since by now in normal cases the freezes would dissappear by itself. /Bjenn

Ye about my last post, it actually was HsMgr.exe and HsMgr64.exe which caused the problem (stuttering). I was playing Heroes of Newerth and I immediately ended those two processes and the problem would go away.
Those two files are from the drivers to my Asus Xonar DX sound card which I wasn't even using in the game, but only in Windows. I maybe will just try to install the ASUS XONAR Unified Drivers (unofficial) and see if that helps.
Here is link: http://brainbit.wordpress.com/2010/07/19/asus-xonar-uni...
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