I agree with above that this is one of the most widely experienced and also most inconsistent issues.
If the issue with your door lock actuators was that they were worn out and slowed down or stopped activating after a couple of presses of the lock/unlock button, then I'd suggest using your free hand to move the door-lock-indicator (the little tab at the top of the door panel that goes up and down to tell you if it's locked (I don't know what it's actually called)) to help out the motor.
When I bought a new remote I was having that issue and finally after a few days solved it with this method. It's not necessarily a sign of bad actuators, it's just a process that puts an exorbitant amount of stress on them.
This thread has all of the steps you need to program remotes yourself, which is handy if you ever need to do it again, instead of paying $85 at the dealership.
__________________
‘98 T100 SR5 4X4 5spd (sold)
‘99 4Runner SR5 4x4 5spd E-Locker Unicorn