Bukkit

What is the issue?

I was editing my permissions bukkit yml code through the console, but when ever I did a commands that changes the config file (/perm player setperm, /perm group setperm, ect):

http://pastebin.com/Pnux36em

Please provide any additional information below.

This is the first time this ever happened

Plugins: http://pastebin.com/yMHMk8f8

Config.yml: http://pastebin.com/AkG7HJ6W

Although the changes appear on the file, they dont seem to be working in game