Player have two groups in the list. When player do a re-login on server, his second group is disappear from his group list each time when he login. No matter which way using to add/set player's groups (manually in permissions,yml, via command or by 3rd-party plugins e.g. Autorank), result is same.
PEX 1.23.4
Spigot 1.11

If you are using Timed groups or permissions, they always disappear when the player logs out.

I'm not using timed groups or perms. Tested on clean server without other plugins, just add/set player's group. Besides, when player logs out this group is not disappear. It disappear when player LOG IN again (re-login).

Pex conflicting with AuthMe... I've been disabled authme and pex works good.
What you suggest to do? I need authme on server.
AuthMe version 5.2 SNAPSHOT

Yes, I've fixed this by disabling permission check in authme config. All works fine.

Good to know it wasn't a PEX problem.