I would suspect the I/o part of ur computer. Check for any suspicious looking process with lots of I/O and mem usage.
I once had a similar problem that won't go away even after reinstalling. My entire comp would get stuck every 3 seconds for almost 1 minute at a time. Wery annoying when u are burning a disk or rendering. I found out that the disk throughput had gone down to < 10MBps. Couldn't track down the problem. But I installed XP from anozer cd and everything's fine.
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http://myxp.blogspot.com
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Winchester 3200+ @2,500MHz
LeadTek 7900GT VOLT MODDED @ 680 core, 1800 mem
2x1GB Transcend DDR400 @ DDR454 2.5,3,3,5,1T
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