Factions Randomly Disabling?

Hello, I am using Factions 1.6.9.5 at the moment, and I am experiencing a problem with this.
At random times when my players try to use a Faction command, it doesn't give permissions for some reason. Most of the times Factions work, but once in a while people just don't have permission for some reason. When this happens, I usually just reload the server and than it works. I know this is a small problem, but if there is some help someone could provide me with, it would be great. I'm not sure if this is because I have an old version of Factions. I tried updating my PEX, but this issue still occurred from time to time. Information about my server is below.

I use PEX, below is a pastebin to my PEX.
http://pastebin.com/yuwC622D

Below is a list of my plugins.
RWtorchLight, Citizens, WorldEdit, NoCheatPlus, ChatProtectionPlus, CoreProtect, DeathHeads, ScheduledAnnouncer2, ClearLag, PermissionsEx, ProtocolLib, Votifier, mcMMO, WorldGuard, Essentials, SimpleVoteListener, ChatManager, EssentialsProtect, DisguiseCraft, EssentialsSpawn, Factions

If there is anything else you need me to provide, please let me know.