Looking over my previous posts, I apologize for maybe not being very helpful. Partly, I did not spend enough time understanding the problem, and part I did not compose my reponse very well.
Before I address the OP's issue more specifically, I want to comment on Srdayflyer's post above.
I expect he is right; the main problem with these tailgates is the wire pass-through from the body to the tailgate. However, using relays likely has some value, regardless of the wire-pass-through problem. Relays are used to take the current load off of switches. Powering a motor, at turn-on there is a large inductive load (current surge) until the magnetic field is established and the motor starts turning. Then at turn off, there is an inductive kick (current surge) as the motor's field collapses and the motor stops. The switch contacts are old and possibly not sufficiently beefy from the factory to handle these normal current surges. Jeep's engineering of these secondary systems was not great.
When you add the relays, you take the load off of the switch contacts and place it instead on the relay contacts. The switch now controls the relay, and the relay now handles the current surges. If switch failure is a problem for these tailgates, adding relays seems like a good idea.
Now to the OP's problems - let's look at the switch in the tailgate.
It is meant to do two things. First, when power comes from the dash control switch to the motor, that power must pass through the switch and go to the motor. Your relays under the dash work because the switch in the tailgate sends the power from the dash to the motor.
Secondly, the switch is meant to activate the motor when you use the key at the tailgate to move the tailgate window up or down. When you turn the key left or right, the switch disconnects the wires from the dash and uses its own power source (power and ground
in the tailgate) to run the motor up or down resp.
With the relays under the dash, there are no wires going to or coming from the tailgate that can be sent to the dash and control the motor. All the control of the motor from the tailgate key switch is
inside the tailgate. There are no external wires to or from the switch, except for 1) the pass-through wires from your dash switch and 2) power and ground that run the tailgate motor.
Realize that, when you turn the key switch, you are disconnecting the wires from your relays (the tan and brown wires). The drawing at the first post in this thread shows you how to add relays that are
in the tailgate. You could put the relays under the dash, but you need to run wires from your added relays to the switch
in the tailgate.
Looking at the drawing in the first post of this thread, control comes from the existing motor wires labeled "+12 up" and "+12v down." These now control the relay coils in the two upper relays. I expect the easiest way to see this is with a truth table -
tailgateRelays.png
UP and DOWN are the two upper relays, connected to the motor up and motor down wires resp. AUX is the third lower relay.
Here 12V is the original motor power that now controls the relays. The polarity of the coil connections does nothing (there is no polarity actually), and is irrelevant. GND is connected to the body/chassis ground. Null is floating, ie not connected as a circuit. Plus and minus are the battery connections in the drawing, used to power the motor.
You can see the power coming from the original tailgate motor wires, and how the output switches depending on which relay(s) you energize. Note the DOWN and AUX relay coils are in series - this seems to be ok, though I would have put them in parallel.
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