I don't know if anyone is gonna read this and this is a very old post but I will post it just in case anyone has the same problem. Once you open to your minecraft directory you will see a folder named saves(as you all know this is where your worlds are saved) in that folder there is a NEI folder(If you have problems in other worlds too delete it, if not let it be) then open the world in which you have the problem(make a back up first, please I don't want to be responsible if something goes wrong) and in your world folder there is a NEI folder too, delete it and run minecraft, I am not sure if this would work but try it.