Personally I had the same symptoms and it was connected to the disk subsystem - either a faulty IDE driver, faulty motherboard or faulty HD. Now this was on a different, Intel, system quite a while back, and the pausing was caused by Windows falling back to PIO mode due to too many errors on the hard drives. Are you using 2k or XP?
I've just been having loads of problems with the nforce4 SATA data corruption bug, which is covered in detail here:
http://forums.nvidia.com/lofiversion/index.php?t8171-0.html
If you can't be bothered reading the whole thread (although it's an idea as different solutions seem to work for different people), it all seems to be to do with the nforce4 choking when too much data is transferred at once over the onboard SATA/ATA channels. I'm probably not explaining it very well!
In your Device Manager, are your drives listed as using DMA or PIO mode (you may need to check the NVIDIA nForce4 Serial/Parallel ATA Controllers instead, listed under IDE ATA/ATAPI controllers)
My problems (DFI UT Expert, SATA-2 WD and SATA-1 WD drives) were solved (hopefully, I am not completely sure they are over) by a combination of:
1. Operating the SATA-2 drive in SATA-1 mode (1.5Gb/sec)
2. Turning on SATA Spread Spectrum in the BIOS
3. Plugging both the SATA and Molex power connectors into both drives
Some of these steps seemed a bit too much like black magic to me but they seem to have worked. Or at least I can play DoD Source and CIV4 without entire machine lockups now.
Sorry this is a bit random, but I thought it might be worth you checking out, particularly if your drives have stepped down to PIO mode.