its not a matter of it messed up root, MF9 blocked the exploit so it didnt work, people saw superuser installed (but not the binary) and freaked out when they had root. no different than people downloading superuser from the market and wondering why it "didnt work". :/
cf-root is pretty cool but only works on devices that can have partitions flashed via a tool. oh and chainfire has to go and manually add in new devices which isnt the easiest thing to get done. exploits work on many devices, but get patched after so long and are not easy to make (the one click scripts are a breeze but the actual hard part, the exploit not so much).
either way, cf-root or flashing recovery and then superuser is the way to go from now on since motochopper is blocked