u will have too wait 24 hours with out running server. after that it should work fine. what has caused this problem is that u probally have been using /reload. dont use that. it screws everything up.
I wouldnt use pex. It is a good plugin for controlling who does what, but the problem is it has a lot of problems. If u reload the server lots of times, it causes pex to disable, making it act up and not having any of the commands work. This is the reason i switched to group manager, cause i will always be able to change tthe deafult perms, and it doewnt have anyy bugs, pex is not as useful as people think