The server is running normally with Essentials vTeamCity, GroupManager, and a bunch of other plugins. The permissions are fine, just as set up. (Example: Admin rank has 14 pages of /help). I drop EssentialsX in and boot up the server, and Admins suddenly have 30 pages of help. They have access to every single essentials command, but GroupManager is still handling permissions of other plugins as normal.

I think it has to do with EssentialsX using vault-based permissions whereas vTeamCity uses GroupManager permissions. I pasted the server starts for each below. EssentialsX seems to be detecting GroupManager, so why is it not adhering to the set permissions for the groups?

Essentials vTeamCity:

[21:22:46] [Server thread/INFO]: [Essentials] Loading Essentials vTeamCity
[21:22:46] [Server thread/INFO]: [EssentialsChat] Loading EssentialsChat vTeamCity
[21:22:46] [Server thread/INFO]: [EssentialsSpawn] Loading EssentialsSpawn vTeamCity
[21:22:46] [Server thread/INFO]: [Vault] [Economy] Essentials Economy found: Waiting
[21:22:50] [Server thread/INFO]: [Essentials] Enabling Essentials vTeamCity
[21:22:50] [Server thread/INFO]: [Vault][Economy] Essentials Economy hooked.
[21:22:50] [Server thread/INFO]: Essentials: Using config file enhanced permissions.
[21:22:50] [Server thread/INFO]: Essentials: Using GroupManager based permissions.
[21:22:50] [Server thread/INFO]: [EssentialsChat] Enabling EssentialsChat vTeamCity
[21:22:50] [Server thread/INFO]: [EssentialsSpawn] Enabling EssentialsSpawn vTeamCity

EssentialsX:

[21:13:17] [Server thread/INFO]: [Essentials] Loading Essentials v2.0.1-b288
[21:13:17] [Server thread/INFO]: [EssentialsChat] Loading EssentialsChat v2.0.1-b288
[21:13:17] [Server thread/INFO]: [EssentialsSpawn] Loading EssentialsSpawn v2.0.1-b288
[21:13:17] [Server thread/INFO]: [Vault] [Economy] Essentials Economy found: Waiting
[21:13:21] [Server thread/INFO]: [Essentials] Enabling Essentials v2.0.1-b288
[21:13:21] [Server thread/INFO]: [Essentials] Using 1.8.3+ BlockStateMeta provider as spawner provider.
[21:13:21] [Server thread/INFO]: [Essentials] Starting Metrics. Opt-out using the global PluginMetrics config.
[21:13:21] [Server thread/INFO]: [Vault][Economy] Essentials Economy hooked.
[21:13:21] [Server thread/INFO]: [Essentials] Using Vault based permissions (GroupManager)
[21:13:21] [Server thread/INFO]: [Essentials] Using Vault based permissions (GroupManager)
[21:13:21] [Server thread/INFO]: [EssentialsChat] Enabling EssentialsChat v2.0.1-b288
[21:13:21] [Server thread/INFO]: [Essentials] Using Vault based permissions (GroupManager)
[21:13:21] [Server thread/INFO]: [Essentials] Using Vault based permissions (GroupManager)
[21:13:21] [Server thread/INFO]: [Essentials] Using Vault based permissions (GroupManager)
[21:13:22] [Server thread/INFO]: GriefPrevention: Hooked into economy: Essentials Economy.
[21:13:22] [Server thread/INFO]: [Essentials] Using Vault based permissions (GroupManager)
[21:13:22] [Server thread/INFO]: [EssentialsSpawn] Enabling EssentialsSpawn v2.0.1-b288
[21:13:22] [Server thread/INFO]: [Essentials] Using Vault based permissions (GroupManager)
[21:13:22] [Server thread/INFO]: [Essentials] Using Vault based permissions (GroupManager)

We don't do anything special with GroupManager, it's handled as a generic Vault plugin with no special code whatsoever other than detection. Can you pastebin your GroupManager group definitions and Essentials config?

Also, can you try setting use-bukkit-permissions: true to your Essentials config, and clearing the player-commands section by setting it to []?

I just tried doing the two things you suggested, but nothing seemed to change. Every other plugin seems to work fine, except Essentials. For instance, if I do /manuadd I am denied access (as it should) but then I can do /smite and /reload where I shouldn't be able to. Using vTeamCity, the same thing occurs unless I add the permission -essentials.* to the default group that they all inherit. Then it seems to work as it should, and denies me access. This "fix" doesn't seem to work with EssentialsX though. Something must be weird with Essentials communicating with GroupManager maybe?

You should be able to view my Essentials Config here:
http://paste.scratchbook.ch/view/9e68370d

My GroupManager Groups:
http://paste.scratchbook.ch/view/6524f163

My GroupManager Globalgroups:
http://paste.scratchbook.ch/view/16fd5b03

Just a note, these are old configs and groups. Our server reset in Dec and the configs are all redone, as well as new groups. But I updated to 1.9 on this old server to test things first. Good thing I did, because I am encountering these issues.

Sorry, saw the team city and hit close too fast.

Can you use the /manucheck command to check what gm thinks you should have permissions for?

As the startup log and vemacs said, we just hook into permissions plugins through vault, we don't do anything special.

Oh my gosh... I am so embarrassed. I did /manucheckp as you suggested, and it turns out the user I was testing with had essentials.* added specifically to themselves. I have no idea why or who did that, but regardless, I apologize for wasting your time. It was my fault entirely.

No worries :)