I'm having a similar problem, but deleting the NEI.cfg didn't fix it. On startup, FML starts, tries loading the libraries, then states "There was a fatal error starting up minecraft and FML."
"Minecraft cannot launch in it's current configuration, pleas consult the file C:UsersJosephAppDataRoaming.technicbigdigForgeModLoader-client-0.log for further information."
The file says this
No crash report is created