This is a major issue with TrinityCore RBAC system in general, not just you. This has happened to me countless times. Only time it stopped working for me is when I restart the worldserver and not the authserver, logging in and out might stop commands from working too -- just never seen it happen to me before. That goes for WotLK and Cataclysm fresh compiles.
They messed up the system and apparently they are too lazy to fix that issue with it. Not much we can do about it sadly.