In the zPermissions permissions class of Essentials. it uses the deprecated methods that use the player's name instead of new UUIDs. While this still works, it requires the server to do UUID lookups each time permissions in Essentials are polled, resulting in server lag:

[Essentials] Lag Notice - Slow Permissions System (ZPermissions) Response - Request took over 140.291ms!
(these can occasionally get quite large, with times reaching into 2-3 seconds)

A fix for this would change the permissions class of Essentials to use UUIDs instead of the player name.