Extremely urgent permissions help!

I've been running this server for two years, and something came up, and I had to entirely WIPE the server. My faction server is the one having this issue. It started like this: Multiverse started to not recognize the world, and then, the server crashed, when I was trying to /reload. After the crash, the entire faction map, (hundreds of bases), was destroyed. In a helpless plea I backed the server up, and completely reset it. I am reinstalling plugins now, and I use LIVECHAT as a chatmanager, and PERMISSIONSEX as a permissions plugin. LIVECHAT is not changing the format of the chat anymore. Also, I fixed the people not being able to build issue, but now no permissions are working, and no titles are present. Here's my permissions.yml http://pastebin.com/TYwF5QX4


Here is my list of plugins...
chatmanager
essentials
livechat
logblock
factions
worldedit
voxel sniper
vanishnopacket
permissionsex
modifyworld
multiverse core, inv, and portals
setrankpex
masterpromote

 

That could be messing up the parsing but I cannot really see anything else that wouldn't work right now.
Anyways, here is the permissions that should work: http://pastebin.com/XdQ7tg6X
Sorry I couldn't help much more :/

 

If you are using live chat with chatmanager as well, that could cause the problem with the formating.

 

Well, with luck, I reinstalled every plugin about two times, with reloads in between. Technically this shouldn't do anything.. But it worked. Thanks anyway!