Like Kyle said, you've got 2 Permission plugins, and that can conflict with tons of things, especially prefix of player. I also recommend removing GroupManager, as PermissionsEx is a more powerful Permission plugin.
Another thing that you could give a try to doing is replacing EssentialsChat with ChatManager that comes with PermissionsEx, so Prefix and chat are more compatible with in game appearance.
I hope some of this has helped. If not, please write back, I'll try to help you even further
You can also add me on Skype, my username is Strychnos27. We can talk on there