I recently upgraded my Dell Precision 390 hack build to Mountain Lion. Only 2 of the four USB ports were working in the rear, while in Lion they all worked fine. Then I remembered that I almost always remove AppleHPET.kext from my Hackintosh builds. Sure enough that was all it took.
Delete AppleHPET.kext (this is frequently a problematic kext when it comes to customac builds).
Ironically, I first found this fix way back in Leopard to fix slow USB speeds.
Using Finder, copy the Kext to the desktop or somewhere as a backup. Better be safe than sorry!
sudo rm -r /System/Library/Extensions/AppleHPET.kext
Make sure to update your kext cache as well.
All ports working – yay!