I have been through thread after thread here on this subject looking for an answer and have tried about everything without luck - but I have some additional details if anyone recognizes them.
My '05 ES330 has never had any problems with its power windows. A few weeks ago - I can't believe I did this - but we had a regular monsoon and I forgot that the windows on the car were down a couple of inches. I went out and closed them before the rain stopped and I honestly don't recall if this problem existed right from the start or only later, after I soaked up the small amount of water that made it to the window switches. The car was not as waterlogged as I'd feared but there was a bit of standing water in the window switch 'wells' where the up-down buttons are.
Problem: rear passenger window goes up and down from that switch, but only goes down from the driver's door switch. (All others working OK.)
1. I have done the reprogramming operation 15 different ways, holding the button 2 seconds and 6 seconds and in auto up and auto down and regular up and down.
2. I have tried the reprogramming from the front door as well (could only do 'down' from there), didn't help, also doing it from the driver's door and at the same time as with the rear passenger door. No go.
3. All window switch lights are on steady, none blinking
4. I took apart the driver's door window switch panel and cleaned up all the contacts. It didn't look bad at all but I did clean the contacts and blew out the area with canned air. Did the same to the rear passenger door window switch. I seem to recall that IT had more water in the switch button well than did the driver's door switch panel. Nothing visibly wrong with either, and again, no change to the problem.
5. I noticed that during the programming operation from the rear pass door that a few times after I did it, going up, the window would only move a very short amount then stop. It would do this over and over if I didn't wait, but If I waited 10 or 15 seconds more, the window went up all the way just fine. The auto full up / down feature works from that switch.
6. I don't know when it happened but the sunroof doesn't open with the remote anymore, while the windows all go down (including the passenger door window). (See #9.)
7. With the rear passenger door window all the way down, if I use the button on the driver's panel, 'down' gets a click (once the window is fully down) but 'up' does not get any response, no click.
8. I've done the 'slam the door while holding the switch' method, also slowly moving the driver's door while holding the switch in case there was a wire that's intermittent, neither had any effect.
9. The battery has not been disconnected in ages but it was run down low by accident a few months ago from me using the stereo for a long time while my wife was in at a doc appointment. That may be the culprit with the sunroof not opening (lost its programming) but I don't recall any issues with the windows til this rear passenger side door window after the rain storm. And I have tried every combination of presses and waits and slams and everything else to get that window to go up from the driver's door; no go. At least I can make it go up by using that door switch but I'd like it to work properly.
Does it sound as though the problem is likely to be the driver's door switch panel?

 

A healthy car battery should power a car radio for 150 to 200 hours. How long was that appointment?

It may have nothing to do with your window problems, but see if you have a healthy battery and alterntor.

 

Hmm, Ford will shut down the accessory power after a lot less than 150 hours, to keep the battery from getting too low - like in less than an hour.
My ES has a Weblink / Sony head unit that plays videos on its screen and my wife was probably at the doc for two hours. Since getting the car jumped and getting the battery charged back up it's had no issues. And I also have a voltage monitor on the car and the charging system is fine. After a startup it runs about 14 volts or a little more and settled down to 13.8 or so after a while. I've done the testing / programming attempts etc. of the troublesome window with the engine running anyhow, so voltage isn't the issue.

I've just ordered another driver's switch panel as it seems to be problem to me, the more I think about it and what I've tried that hasn't worked to fix it the window issue.

 

Exchange the left rear window switch with the right rear, see if the problem follows the switch.

When operating the rear window from the master switch, power must pass through the rear window switch before reaching the motor, a failed rear switch can cause your problem.

#5: The window motor is getting weak, that is why it must cool before it will continue raising the window.

The sunroof likely needs to be initialized after the dead battery incident.

Power draw on the battery with the ignition in the "accessory" position while operating the radio is almost 10 amps, 2 hours is beyond the safe limit.

 

A toaster oven cranked up will draw 10 amps. A car radio will not. Usually about 0.5A if sitting listening at reasonable volume.

Two hours listening to music should not impede a healthy battery. At all. This is a clue there may be other electrical problems, and a solid diagnostician makes sure there is a good baseline in any system first. It may NOT be an issue, but a simple alternator test with a multimeter is in order.

 

I think that's a great idea and very easy to try, swapping the switches. I'll try that.
I agree with you, really didn't think a car battery could run a car radio / audio unit for 150-200 hours! I hadn't realized how low the battery had gotten that day. I now have a 'jump pack' in each of my vehicles.
**UPDATE**
That was a great suggestion and easy to do - but it didn't make any difference which switch was on that door's window, both worked exactly the same there and from the driver's door.a Hopefully the replacement driver's switch panel I ordered will fix it.

 

Manual for my Sony XAV-7000 says rated power consumption, 10 Amps. Given my results in real life it's certainly closer to that than to .5 A.
I wasn't playing at anywhere near the full power but that would be 45x4 or 180 watts, about 15 amps. I think it's drawing morfe than .5 amp if I just turn it on and don't play anything on it, video or audio.

 

“Rated” power is nothing like what is actually being used. That’s akin to saying that your GS engine is rated for 302hp, and assuming that’s what it’s making when you go 25mph through a school zone.

If you retro-fit a multimedia center like that in it, it will draw much more but should not kill a battery that fast unless a weak ground or other issue. Power draw for sound production is a massively log scale; as long as you were listening at normal volume, it would draw under 1A, especially if stock audio (still unclear on that).

Your car is old enough and this specific comment indicative enough, it would be wise to simply check for charging voltage and also A/C ripple voltage with a multimeter, and perhaps parasitic draw to verify the aftermarket radio (if installed) is properly grounded. The AC voltage, if present, could also explain the programming issues. Again, it may NOT be the issue, but there are questions here that leap out if you understand alternator function, regulator diode failure characteristics, and battery capacity characteristics.

 

Well two things: first I got a new set of driver's door panel switches and now all the windows are working fine.
And except for one day watching video and playing the audio system for a couple of hours, never had another problem. The charging voltage is in the mid-14's after a period of using accessories with the engine off, it's low 14's dropping to upper 13's otherwise.
No problems.