Allright, I'll go ahead and Ass U Me you meant 99. So the back window motor is controlled by the Back door ECU. Which is powered by two circuits one hot all the time and one hot with ignition on. It also gets signals from the Body ECU which in turn receives signals from the switch in your dash. The switch in the lock cylinder on the rear door however is connected directly to the Back Door ECU (BD ECU).
The highest probability for this problem is in the BD ECU or the Rear switch. It would be very hard to trouble shoot if you don't have the problem actually happening. But there are some things you should look at.
1. The easiest is the connector for the harness to the rear door from the body. You need to make sure it is not damaged, either corrosion or chaffing, or even burnt or cut wires. This is a common problem on 3rd gens, although I hadn't heard of your symptoms.
2. You should remove the trim panel, and the black metal panel covering the guts of the rear door. Then inspect the connectors for the BD ECU, and rear switch. Hopefully you can find some evidence of the connectors having moisture or something that would cause a circuit to "short" Or maybe the switch is getting stuck.
This would be a great start, sorry I don't have the silver bullet for you.
:couch2: