Try the following:
1. Launch KOTOR2.
2. Before starting a new game, or loading an old one, ALT-TAB back to Windows -or do something else to bring up the Task Manager-.
3. Bring up the Task Manager, unless you have already done so (CTRL-ALT-DEL key combination or right-click on the taskbar).
4. Click "Processes".
5. Right click Kot0R II process (swkotor2.exe), and somewhere there should be an option Set Affinity - select CPU 0 or deselect CPU 1 (Windows should now only be using one core for KOTOR2).
6. Go back to the game and see if this helped.