from my basic understanding of reading the readme file for WoWME:
1) Run WoW with WoWME.exe
2) Once you reach the login screen, hit F8 to restore changes
3) Login
4) Have fun
So i make the basic assumption that you run both, or am i wrong? Either way its not working for patch 3.2, getting an error on the # of lines in a character file (male Draenei to male scourge)