As far as 'Journeys End' goes, its a matter of what counts as a used regeneration. Certainly he used the energy to heal himself then siphoned the part off that would have changed his body. So if we go by how many times he can use the regeneration energy then he has used one in that episode. That said, maybe a regeneration is only counted by a full body metamorphosis and not the energy. Thing is, we don't know for sure.
We know from LKH that the energy is finite as it took all of River's energy (and this her remaining lives) to heal the Doctor. So the indication is the energy level is what dictates the limit, so when the Timelords offered to give the Master a new life cycle they were perhaps just going to 'fill' him up with the energy that would last 12 more regenerations.
Where the doctor is concerned, for all we know the Timelords could have 'filled' him up, so to speak, to help fight the time war. A simple throw away line about that would explain it.