Problem/Bug PermissionsEX/Essentials Help :)

Hi there!
I have been making a Prison server for quite a while now and seem to have several problems with PermissionsEX and maybe Essentials. (All server info will be at the end of this post. )

1. Prefixes appear twice. (Permissions file below)
2. Rank A-Free cannot eat food. (Screenshots below)
3. Groups do not have permissions that I have put in the permissions file. Only the ones added in-game using commands work.
4. Ranks A-Free do not have permission to use tools or ender chests/chests/crafting tables/furnaces.

Those are all the problems I have noticed so far. Please could somebody help?
Thanks!

--Extra--
Permissions File: http://pastebin.com/hxTbesfC
Screenshots: (All problems are in the two screenshots)

 

Im looking forward the bond of PEX and Essentials... ill let you know when i find something, but for now I advise you use GroupManager plugin

Stay Cool, SDL