you could also have a look to the executable x3 size when you play, to see if their is a probleme with the memory usage, if the thing take more that 2 GB for X3 then their is a memory leak issue
also just give a try in windowed mode, this will disable AA and maybe others stuff, just to see if the problems are still here in windowed ?
New Config : Intel 8400 & 4Ghz , 4GB DRR2 on Asus P5Q Pro, ATI 4850 and Win XP 32 bits SP3.