Fixed: http://pastebin.com/EBPtsLgG Your permissions.yml formatting was completely messed up. Pay attention to the difference between mine and your old one. I suggest sticking to adding permissions/groups in-game so that you do not break your permissions.yml file.
I believe it the problem was to do with your spacing, as there was a lot of spacing that was off/messed up. I have tried to the best of my ability to clean up the file, and I have uploaded the possibly fixed file to pastebin, which you can find here: http://pastebin.com/yJ96gtqt - this file should fix all of your problems. Please post if it does not. =)
I had originally been fixing his file, and had posted close to the exact same time as you; I don't believe that your corrected file is bad, and it was corrected in the exact same way mine was.
@Apathy Oh that's weird, I didn't get an email until a while after (I have emails enabled for all replies to all threads I post on). I didn't notice that you posted right after me, my bad. Nonetheless, OP marked as solved so our job here is done