I don't use AC, but the other apps I use that need root (ROM manager, CacheMate, TiBackup etc.) are listed in the SU app with a green dot next to them. You might try to clear everything out of the list in SU, reboot and let all your apps re-ask for permission.
My other thought is to go into settings and clear the data for SU. I don't know if that would hurt anything or not, it shouldn't...
EDIT: Additional thought, have you repaired permissions recently?