Every time I restart the Server My file is ok but my users dont remain in the groups they are set to. Why is this happening?

Having the same problem over here

28.11 20:51:19 [Server] Server thread/ERROR [Sponge]: Could not pass FMLPreInitializationEvent to Plugin{id=permissionsex, name=PermissionsEx, version=2.0-SNAPSHOT-b145, source=/mods/PermissionsEx-Sponge.jar}

Unfortunately PermissionsEx is currently unmaintained and no further updates are planned. Because of this, all pull requests are being closed. If you are looking for an actively maintained permissions plugin, take a look at LuckPerms. It is compatible with major server platforms and can import data from PEX.