Groups plugin: PermissionEx
EssentialsX version: Latest dev.
EssentialsXChat + 1 groups added player = Groups format work.
EssentialsXChat + 2 groups added player (1 group not set prefix) = Use Default groups formating, and not work group formating. (Spigot Essentials = work)

What permissions plugin? Do you have Vault installed?

Group(Permission) plugin: PermissionEx.
Vault installed

Startup log, screenshot of issue. Does this happen with Spigot-Essentials chat? (You can mix and match)

https://www.youtube.com/watch?v=w0s6I0iXBbQ&feature=youtu.be

Config:
chat:
radius: 0
format: '{DISPLAYNAME}: {MESSAGE}'
group-formats:
Admin: '{DISPLAYNAME}&8:&c {MESSAGE}'
Tulaj: '{DISPLAYNAME}&8:&c {MESSAGE}'
Moderator: '{DISPLAYNAME}&7:&b {MESSAGE}'
Old: '{DISPLAYNAME}&4:&6 {MESSAGE}'
Tag: '{DISPLAYNAME}&3:&f {MESSAGE}'
Premium: '{DISPLAYNAME}&8:&f {MESSAGE}'
Vip: '{DISPLAYNAME}&6:&f {MESSAGE}'
Vip+: '{DISPLAYNAME}&e:&f {MESSAGE}'
Elit: '{DISPLAYNAME}&a:&f {MESSAGE}'
Helper: '{DISPLAYNAME}&6:&f {MESSAGE}'
Foepitesz: '{DISPLAYNAME}&9:&f {MESSAGE}'
Epitesz: '{DISPLAYNAME}&9:&f {MESSAGE}'

Startup log?

[16:27:05] [Server thread/INFO]: [Essentials] Enabling Essentials v2.0.1-b192
[16:27:05] [Server thread/INFO]: Using locale hu
[16:27:06] [Server thread/INFO]: [Essentials] Using 1.8.3+ BlockStateMeta provider as spawner provider.
[16:27:06] [Server thread/INFO]: Using locale hu
[16:27:06] [Server thread/INFO]: [Essentials] Starting Metrics. Opt-out using the global PluginMetrics config.
[16:27:06] [Server thread/INFO]: [Vault][Economy] Essentials Economy hooked.
[Multiverse-Core] [AllPay] - Version 13.0 - hooked into Essentials Economy for Multiverse-Core v2.5-b691
[16:27:07] [Server thread/INFO]: [EssentialsChat] Enabling EssentialsChat v2.0.1-b192
[16:27:09] [Server thread/INFO]: [EssentialsGeoIP] Enabling EssentialsGeoIP v2.0.1-b192
[16:27:09] [Server thread/INFO]: [EssentialsGeoIP] This product includes GeoLite data created by MaxMind, available from http://www.maxmind.com/.
[16:27:09] [Server thread/INFO]: [EssentialsSpawn] Enabling EssentialsSpawn v2.0.1-b192
[16:27:13] [Server thread/INFO]: [AuthMe] Hooked correctly with Essentials
[16:27:13] [Server thread/INFO]: [AuthMe] Hooked correctly with EssentialsSpawn

Full log, not just a truncated section, uploaded to a pastebin service. Note that we (and Vault) don't support cracked servers.

http://pastebin.com/rNt59Tip

Does this issue occur when you make your server not cracked? I'm not seeing a permissions handler properly registered in your startup log.

[16:26:56] [Server thread/WARN]: [PermissionsEx] This server is in offline mode. Unless this server is configured to integrate with a supported proxy (see http://dft.ba/-8ous), UUIDs may not be stable!