I used to have that problem frequently on my Tacoma, but it hasn't happened on the 4Runner, however maybe they share components? The motor that actuates the lock was inside of a small white plastic subasssembly, and it used tiny little gears – like the ones on a small toy car. From time to time the grease they used in that subassembly would thicken in viscosity and bind up the mechanism to the point that the door would only lock/unlock with the key. I never replaced it, as taking it apart and cleaning/regreasing seemed to solve it for a time. Just thought that was worth sharing, in case that's what's happening to you.