Problem/Bug Essentials /list and /spawn do not work. PermissionsEx Error?

Hi, I am using the latest version of essentials. I've recently noticed, the command /spawn and /list do not work. I've tried uninstalling it, and re-installing it, deleting configurations as well, but I've had no luck. I know a bit of code to tell its something with permissionsex creating a problem, but I don't know what. Can someone please help me? The error I get when doing the commands is "Error: 0" in a dark red color (&4).
Console Startup:
http://pastebin.com/QCLQ79CT
Plugin List:

Permissions.yml file in PEX:
http://pastebin.com/F4Sbx9Cc

 

@Rockdude_, lets make this simple, your server is severely screwed up.

1) you have two different versions of protocalib installed. Delete one.

2) I have no idea what would cause this to happen, but it's bad.
15.02 21:02:10 [Server] INFO at org.bukkit.plugin.java.JavaPluginLoader$1.execute(JavaPluginLoader.java:298) ~[spigot-patch-1.8-20141113a.jar:git-Spigot-1.7.9-R0.2-208-ge0f2e95]
Possibly the updater?

3) You're running the 1.7.9 version of the jar, and yet this is trying to use a 1.8 config system

1. 15.02 21:01:21 [Multicraft] Loaded config for "A: Spigot 1.8 (Patched 11/13a)"
2. 15.02 21:01:21 [Multicraft] Starting server!
3. 15.02 21:01:21 [Multicraft] Loading server properties
4. 15.02 21:01:21 [Multicraft] Received start command
5. 15.02 21:00:57 [Disconnect] User Rockdude_ has disconnected, reason: Server shutting down
6. 15.02 21:00:57 [Multicraft] Server stopped
7. 15.02 21:00:55 [Multicraft] Error writing to server: [Errno 32] Broken pipe
8. 15.02 21:00:55 [Multicraft] Error writing to server: [Errno 32] Broken pipe
9. 15.02 21:00:55 [Multicraft] Stopping server!
10. 15.02 21:00:55 [Multicraft] Server shut down

4) You're running the protocalib for Bukkit, not spigot.

5) You need to update PermissionsEx

Anyone know what num 2 is being caused by or see anything else?

 

Thanks for the analysis. I believe it it permissionsex, because when I installed that I believe the problem began.

 

@Rockdude_, not a problem.

 

@Tecno_Wizard I'm now having issues installing pex. It turns red and disables, any suggestions?

 

@Rockdude_, can you post what you are seeing in the console window? It's hard to know what red means when I don't know what it said.