PermissionsEx stopped working after a reload?

Last night I finished up configuring a few plugins, and I sent the plugins folder back to my host. Pex had stopped working before, so I decided to fix that along with other things. Anyways, when he stopped the server, replaced the old plugins folder with the new one, and opened it again, pex worked. There was just a problem with a different plugin, PrisonRankup, that he had to fix. When he fixed it and reloaded the server, pex didn't work. I did /pl, and PermissionsEx was colored red instead of green like all the other plugins. We tried making sure all of the plugins were 1.7.2, we tried using a yaml parser to check if there were any mistakes in the file(there weren't any), and now I don't know what else to do.
He checked the console, and it said pex loaded fine, and that it was enabled. It still isn't working.
The plugins I have:
WorldEdit
Reward Voting
CoreProtect
Vault
ClearLag
PermissionsEx
PlotMe
Votifier
WorldGuard
PrisonRankup
Block(Items to blocks)
Essentials
ProtectionStones
EssentialsSpawn
EssentialsChat
Multiverse-Core
MineResetLite

Here are my permissions: http://pastebin.com/0bN9Gcbi

 

TamaPookie Your owner group has their prefix and suffix lines under the options section; they shouldn't be there. Same thing with your premod group, suffix does not go under options. Fix the spacing on those and it should fix the file.

Just a side note, don't /reload your server. That can break things sometimes. If you have a plugin that has its own reload command, like PEX has /pex reload, that's fine and won't hurt anything. Otherwise, it's better to /stop your server, fix whatever needs fixed, and then /start it again.