My best guess is a problem with your permissions.yml. Could you pastebin that and the startup section of your server.log?
I decided to look at it, it did turn out to be that my Permissions broke and all my plugins and Bukkit went nuts! I have fixed it and just thought it was more serious.
Here is the first part of the log. I'm also getting a PermissionsEx error, could that be the problem?
I'll answer more questions when I get them.
--AnUnknownMiner
My best guess is a problem with your permissions.yml. Could you pastebin that and the startup section of your server.log?
I decided to look at it, it did turn out to be that my Permissions broke and all my plugins and Bukkit went nuts! I have fixed it and just thought it was more serious.
--AnUnknownMiner