I fixed this by disabling ChatEx, but now only one prefix appears.
PermissionsEx allows you to specify what commands certain players are allowed to type.
I could send you a copy of one of my backed up permissions files if you'd like to take a look at it.
Modded Forge servers, on the other hand, generally do not use permissions.
There are no permissions cause I am not gonna set and test them until later, btw.
However, operator in singleplayer world must have command permission level of 3, because its Operator Commands is enabled.