Here are the things we tried:
1. Uninstalled and re-installed video driver.
2. We went to BIOS setup (F2 on startup), Integrated Devices> Video Controller, then we changed AGP to AUTO.
3. We even reseated the video card and CMOS coin battery.
All these didn't make a difference. It's true that ATI Control panel from the old GPU won't uninstall so this may also be causing the problem. Upon research we stumbled upon a forum http://discussions.virtualdr.com/archive/index.php/t-231257.html
posted by MPTECH
I finally contacted MSI and here's what they told me:
Ensure you have latest Bios update for your board (If you have not done so already). Please try with clearing the cmos setting on Jbat1 jumper/SW1 Switch or removing the battery on the mb out for 1 minute and put it back in with power off. Turn system back on load optimized default setting in bios cmos, save exit. If you didn’t start out with a clean/fresh load of Window please do so for best result.
We ended up doing so and it worked. Thanks MPTECH!