The next most common problem, at least in 1st gen 4Runners, is a missing shell interlock bolt (image D above - bolt A below). These are the two funny looking bolts near the back. If they are missing, the relay thinks the top is off and won't let the window move, up or down. If the bolt is installed and you still suspect a problem, pull off the trim/panel on the driver's side and look at the interlock switch. Sometimes, if too long a bolt was installed, the switch can become deformed and may no longer work properly. Some folks just wire a jumper across this switch to bypass it.
4Runner Rear Window Cheap Tricks