'03 Q.

Yes, I can read a wiring diagram, have the FSM, but the way it's broken into pieces, I'm not seeing what I need to. It may or may not be there.

Front pass door. Sometimes the auto up function works, sometimes it doesn't. Yes, I've done the initializing a couple of times. But also, I've had problems over the years with the alarm system and in fact have at times triggered it washing the car by spraying water at the door/fender area. Had enough problems over the years I've disconnected the horn portion, but I'm getting an occasional dead battery, and I mean dead dead, no dash warning lights at all. I think from the alarm triggering the headlights. I'm guessing it's related. But since I park it across the street and don't see it that much I don't really see it happening.

But what would intermittently enable/disable the auto up function and could it also affect alarm operation?

Most of the old stuff had lock cylinder switches on both sides, so if you have a passenger cylinder, there's a good chance the switch is shot and taking water. That wouldn't affect the auto function, but is it out at both switches? If auto works from the master but not the slave or vice versa, chances are it's a worn out switch.

Nope, lock cylinder on drivers door only. And the auto works/doesn't work on both sides at the same time. It does the go up, then bump down 6 inches if you hit auto. Sometimes. But auto function will return without a reset, just randomly. And yes I know about using the mid point contact to get it to go all the way up, although my wife struggles to understand it.

I suspect the two functions, window and alarm, are related, I just can't figure out how as I don't see a full wiring diagram for the door, just partial functions.

If the window is backing itself down then it thinks something is pinched, but mechanical resistance in the tracks or regulator can cause the anti-pinch to operate falsely. First thing I'd try is some high-vis silicone in the tracks. If that doesn't help, your regulator may be going south. I really can't see how the alarm could be related unless something is south in the wiring, have you checked the umbilical and door connector(s) to make sure there isn't a leak into the kick panel?

No, it's not a pinch function. It's definitely something that has to be programmed in. If I pull halfway up on the PW switch, it will go all the way up. There's a procedure, something like pull the door panel, run the window all the way down, then push on a little button on the motor assy and motor the glass all the way up. Something like that, don't use that as the procedure. More or less, just not the pinch function.

There isn't an obvious problem with the harness from the body to the door, nor have I dug in really deep, I'm trying to figure out the logic in it before I go in deep so maybe I know what to look for. What's the umbilical, and no I haven't dug into the kick panel that much, but I have been in there.

The umbilical is the bundle of wires connecting the door to the car. Maybe I misunderstood, but you seemed to imply that the window was retracting by itself after it hit the top. Anti-pinch is the only thing which will do that, assuming the window is already calibrated (the little button behind the panel which you referred to). That system works by correlating the encoder position (set using that button) with the amount of current drawn by the motor, which will climb precipitously when the motor stalls. If it sees a stall at an encoder position which isn't at the top, it assumes something is pinched in the window and backs down several inches. It's also possible the encoder has failed and will take a calibration but won't hold it, and also possible the motor is worn and drawing stall-level current at a lower than normal load. Both of those conditions would mean a new motor.

Yes it does retract when it hits the top. Sometimes, but only if I use the auto up function. But if I use the intermediate switch position instead of the auto, I can run it up every time without problems. I wasn't aware of exactly how the system worked, I guessed it was a counter of some sort. But it comes and goes, as does the interior light coming on for no apparent reason. The interior light coming on semi randomly would account for the alarm problem, but it also seems to be tied into the window problem. So I'm trying to find something they have in common. I pulled, tested and replaced the door switch, but it was when I was spraying around the door/fender junction at the front of the door I could make the alarm go off, which would suggest the switch by the back of the door is not the problem.