Every time I update my Hackintosh (P5WDH mobo) with the latest version of Mac OS I lose USB 2.0 speeds (all ports go to 1.1 speeds) and my system refuses to completely shutdown. The fix:

Delete AppleHPET.kext from /System/Library/Extensions

USB is flying and my systems sleeps and shuts down!

Quick and dirty:
Using Finder, copy the Kext to the desktop or somewhere as a backup (or you can use OSX86Tools too). Better be safe than sorry!
sudo rm -r /System/Library/Extensions/AppleHPET.kext