I think I have the same problem...
I used to play KOTOR2 on my old PC without any problems...but as soon as i bought a new PC (Win7 Professional x64) and installed KOTOR2, i had few issues to deal with, but this is making me mad...after I start KOTOR2, game runs fine for about 2 minutes...then I start to have horrible lags every 10 seconds...lags like on Dantooine (but i have them everywhere) You know, i just move, it freeze and I am on the other side of map....and this happens everywhere, in combat, main menu, conversations...I tried everything I found on internet...running as administrator, Disable Vertex Buffer Objects, updating drivers (ATi HD5570 card), patching game, reinstalling game (about 6x) but nothing really helps...
Any suggestions please?