Open your server.log file and copy and paste in "CODE" form on this thread.

Then I can see whats going on.

Also copy and paste your permissions file and paste it here: http://yaml-online-parser.appspot.com/

I'm having major trouble with this issue. I hope someone finds a "reasonable" answer basides getting rid of some plugins...

Ok mate, PermissionsEX and Factions and Essentials DO WORK. I am running all three of those right now on my server and have been for a couple of weeks. I had this problem, but I think it was before of McMyAdmin with my VPS provider. I had to install 'iChat' a plugin that displays prefixes. It displayed prefixes that you tell the plugin to make and also shows faction tags.

I am running Essentials Spawn and Essentials. Non of the other Essential.jar's

You need Essentials Chat.

Ok, I will list all the plugins I have for you:

PEX
Factions(I just uninstalled it)
WorldEdit
WorldGuard
NoCheatPlus
Vault
ButtonWarp
AutoRank
Essentials
ChatManager
MotdManager
War
mcMMO
LogBlock
MobArena
ModReq
EmergencyDowntime
Multiverse-Core
PerformanceMonitor
DeathMsg
EssentialsSpawn
ModifyWorld
MagicSigns
ToggleInventory

you need "essentials group manager"

This sometimes is a common mistake to make

bump

Why no one help

Can someone else help me?

I only have Essentials and EssentialsSpawn. That's all the Essentials plugins I have.

Do you have any Essentials plugins? If so can you name them.
When i used to run a server i had the same issue, prefixes weren't showing and what-not. It worked when i deleted an Essentials plugin.

Anyone else know why they're not working together?

I don't understand why they don't work for me. The prefixes just disappear and no one has permissions except OPs

They should work fine.