Make sure your tailgate is fully latched as there is a limit switch in the latch. I think it needs two 'clicks' on both sides.

Mine had an issue where the left side was half-latched but the switch made contact until the window was almost up then it pushed the tailgate open just enough to break the contact.

1989 4Runner Special Edition
22RE, 5-spd.
TG 3" SAS, MC DuaLs, 4.56s, Air Locker
Hi-Clearance panels by
www.toyotafiberglass.com