Check out the manual again.
When I went to pick up my 4Runner, the rear hatch would not operate by fob or with the key in the rear lock.
You have to reprogram that window if battery is disconnected, etc. by using the control on the dash. As I recall you raise and lower the window fully then walla, it works.
I also had to do this when I installed a new head unit.
It is mentioned in the manual somewhere...
When I went to pick up my 4Runner, the rear hatch would not operate by fob or with the key in the rear lock.
You have to reprogram that window if battery is disconnected, etc. by using the control on the dash. As I recall you raise and lower the window fully then walla, it works.
I also had to do this when I installed a new head unit.
It is mentioned in the manual somewhere...