How did you root it the first time? Is USB Debug checked on the phone? I've plugged my Atrix into Windows XP and Windows 7 x64 and had no issues with the phone being recognized.
You might want to set USB to Phone Portal and see if that will install drivers to your system, then just switch back to "none" afterwards if it does install. Also, if you're using a USB hub, try going straight to the back of your PC instead.