Caydr,
Our systems are very similar:
Shuttle SD39P2 | Intel Core 2 Duo Conroe
[email protected] GHz (320 FSB) | Crucial Ballistix 2x1024 MB PC2-6400 DDR2 (@800, 4-4-4-12, dual channel mode) | NVIDIA eVGA 8800GTS 320 MB | Maxtor 320 GB SATA II (7200 RPM, 16MB cache, AHCI mode) | NEC ND-2510A dual-layer DVD-R drive | Mitsumi FA404M floppy drive/card reader | WinXP Pro SP2
Sins plays absolutely great. I run it with everything maxed out, with 4x AA, at 1280x960 (I have a CRT), in 4v4 games online via ICO with 3 friends, on large galaxies, and don't have any problems (except for the bug Annatar has mentioned, which appears to be a Malice issue).
My first question is this: have you tried turning off all the overclocking? This can cause some weird nonsense in games. For example, I have a problem in Crysis where after a while the textures start to get messed up. No other game exhibits this behavior, and while I have personally not tried to run the game at stock clocks yet, I suspect it's the issue.
I can't guarantee this is the problem, but it should be ruled out. Make sure you back your CPU to stock speeds, your RAM timings, and any voltage boosts that you had to give the hardware to make it run at those speeds.
-HM