This is just conjecture.
I have the same problems here too. I've recently installed a 9800 pro after my Ti4200 died. The performance was pretty good on old stock cat 4.x. Performance dropped once I went to 5.12. Noticing how sluggish the Command center was, I closed it down. This improved the performance a great deal. A friend of mine even went as far as setting up his card, then removing the CCC completely (you lose adjustment features after)
The CCC uses the .Net framework which is not the speediest of things. If it's polling the system for changes etc this may be where the problem lies.
I don't think this is just an LFS problem. Try disabling the CCC before LFS and see how you get on.