The addition of the Randomiser to the Tardis controls in 'The Armageddon Factor' shows that the Doctor could navigate at that point. The First and Second Doctors never could.
The Third did manage to set course successfully to Metebelis Three. I'd suggest that when the Time Lords unlocked the secrets of the Tardis at the end of 'The Three Doctors', the Doctor used the opportunity to finally fix the navigation systems. Even if that particular information hadn't been suppressed, Three apparently had greater technical skill than his previous incarnations. Access to the UNIT laboratory, primitive though it was, might have also given him an opportunity to carry out repairs, something he may earlier have lacked.