Fireseal, I also have a Q9450 with 4Gb DDR3, but running on a 790i m'board with twin 9800 GTX on Vista 32 (so less available of the 4Gb.) All drivers are up to date and like you, Crysis, Grid, Supreme Commander, etc run smoothly at max settings - as you'd expect after spending this much on a PC! Sins (patch 5) is the only game that just doesn't want to play.
Even with 4 opponents on a medium map, the game slows down massively once the AI players begin building their fleets. When loading a savegame from the previous evening the effect is immediate, so it's not a gradual thing. At its worst, I get 5-10 seconds of smooth play, then everything but the mouse cursor and music stops for anything between 30s and 2 minutes. It's entirely unplayable. I have also noticed that exiting to the main screen from the 'game stats' screen takes around 5-10 minutes. There are no error messages, the game doesn't crash, it is simply unplayable.
I've tried dropping resolution, switching every effect off, switching absolutely everything to minimum, stopping all other tasks running on the PC, setting the game affinity to every conceivable combination and permutation of cores, running as administrator, running with and without SLI, etc. Nothing makes any difference. Memory, processor load, HDD load, etc are all normal (i.e. not 100%) and vary with each test I do - so they don't seem to be part of the problem. Had it been a memory problem, I would have expected the pagefile to go ballistic, but this isn't the case. Processor and graphics temperatures are all fine so its not a heat issue. I have tried everything I can think of and can only come to the conclusion that it's the game itself.
Any admins out there with a clue why this is happening? There are 2 of us with very powerful machines that should be able to run your game without any problem, but in both cases the game slows to less than a crawl. Why?