Horrible video skip / lag problem - once per second in all apps!

Question

 I built a new system last month (my first AMD) and I am having a really aggravating problem. In all games and all video playback I get an annoying skip once per second, every second. It affects sound during gameplay but not during movie or mp3 playback. It even happens with the visualization mode in Windows Media Player.
My system is as follows: MSI K8N Neo4-F, A64 3200+ venice core, MSI 6800GT 256MB PCI-E, two sticks of Corsair valueselect DDR400 512MB each, 500 watt PS, 160GB 7200 SATA HDD. Most recent NVIDIA drivers for everything. WinXP Pro with SP2 and all updates, DX9C. Nothing overclocked, all settings standard.
I have tried the following solutions:
1) BIOS upgrades, started with 1.4, installed 1.5, MSI tech support gave me 1.6b2 and I installed that. No luck with any of them.
2) Memory, installed per MSI directions, but I've tried all legal combinations, including one stick at a time. No change.
3) full format and reinstall of WinXP. No luck.
4) Switching between WinXP IDE drivers and NVidia drivers, with and without RAID drivers, No luck.
5) Removal of 6800GT PCI-E card and replacing with Ancient 8MB PCI Permedia2 video card. Problem still persists.
6) Disable onboard sound and LAN. No luck.
7) Running Fedora core 4 on second partition. Installed Nvidia video drivers, tried some games. THIS WORKS! No hitch, no skip, no nothing. Framerates are noticably slower but very stable. In WinXP I saw framerates bounce all over the place, from 230 FPS down to about 70 with one game. That same game on Linux ran smoothly at about 166 FPS with only occasional slight drops. The big FPS drops in Windows usually came right after one of the skips but didn't occure after every skip.
Right now I'm stumped. Linux uses totally different drivers for sound, LAN and SATA support. Some of those drivers don't fully use the Nforce4 chipset's features, maybe that's part of the difference.

Answer 1

Thanks TireSmoke:
I had found that sticky, but I took your advice and went thorugh it in detail last night.  Lots of great info, fixes tweaks and tools, sadly none of them fixed my problem.  The lag problem most people are reporting is not really like the wierd problem I am having.  I have tried the recoommended fixes with ablsolutely no change in my system's behavior.
I am beginning to suspect a faulty motherboard component.
Russ_XP:
I think you are correct about fast writes.  I googled the heck out of that last night and couldn't find any reference to enabling or disabling fast writes on PCI-E.
The drive is SATA-1.  The Neo4-F is not SATA-2 enabled (there is a hack for it though).  From memory I think it's a Western Digital WD1600-something, 7200 RPM dirve.  I've tried it on both SATA buses and tried disabling the unused bus in BIOS.
I'm pretty sure I can dig up an old PATA drive somewhere and give that a try.
Gpalmer:
True enough, and I don't have these problems under Fedora.  Sadly this is a cross-platform game development box, I need both XP and Fedora working.
Black_God:
Nope, this is a clean install.  Although I wonder, could any of the built in XP update and security tools be causing this?  I have disabled Windows firewall and virus protection monitoring.