Driver window clunk when shut fully after using AutoDown and it's hot outside

I'm looking for any advise, thoughts, and whatnot here. I'm still working with the dealership, but we're both kinda stumped.

I've got a 2014, Double Cab, Baja Edition with 8,000 miles on it that I bought new in April. The driver's side window makes a clunk noise when it I put it up all the way. The clunk happens when the window is shuts fully or is just about to shut fully - it's really hard to tell. Also, sometimes, even when it does not make a clunk, the window seems to shut awfully hard (i.e. when it closes fully, it's like it almost slams shut, if that makes sense).

The clunk happens pretty regularly when it's warm to hot outside and I've used the Auto Down feature to put the window down. It doesn't happen, or it's pretty intermittent, if I hold the button down to put the window all the way down. And, it doesn't happen if I put the window down part way and then put it up.

I do not remember when it started, but with the warmer temperatures here in Texas it's been happening more often. One other thing to note is that I have installed WeatherTech Window Deflectors, but it happens even if I remove the deflector.

Last Thursday, I brought the truck to the dealership to have it looked at. At that point, I had not realized the noise happened more regularly when it was hot outside and I hadn't figured out that it was associated with using the Auto Down function. I just knew it made a noise intermittently and it was getting worse.

The tech worked on the truck that morning and did get the noise once or twice, but after some adjustments and removing the deflector, he felt he had it fixed. Unfortunately, when I picked up the truck that afternoon, the noise was back.

So, we got the tech out there to look at it and it was then that we realized it was associated with the Auto Down. So, he worked on it that afternoon and eventually burned out the motor. So, they kept it overnight so they could get a new motor in.

Friday morning, the tech replaced the motor and there was no more noise. Unforuntanetly, when I came that afternoon to pick up the truck, the noise was there again (without the deflector). It was at that point that we figured out it being hot outside had something to do with it. We decided I would bring it in again on Monday (yesterday) and they would look at it and possibly replace the regulator.

So, yesterday, they worked on it, but do not replace the regulator. Instead, they noticed there is a part of the molding that moves a bit when the window goes all the way down. And with the deflector in, and it being hot outside, that molding sticks to the deflector and can't move back into place like it should. So, when it finally does move into place, it makes a clunk. That was the theory. The service adviser even showed me a part of the molding that has a "bump" in it and when he pulled it out, you could see where there was some wear.

At that point, I was pretty tired of dealing with the problem and the window was not making the clunk. So, I took the truck home and decided I would see what would happen with the deflector not installed. Sure enough, the window did not make any clunks the rest of the day yesterday (it really wasn't hot outside) or this morning, when it was in the 70's and 80's. However, this afternoon with the temps getting into the 90's and with the deflector still NOT installed, the noise is back.

My plan is to give it a couple more days and then contact the dealership again. But, I was wondering if any of you have any ideas or have seen anything like this? I did take the door apart yesterday afternoon to see how the mechanism operates and in hopes that it would make the noise and I could figure something out. But, I didn't see anything wrong, no binding, no nothing, and, of course, there was no noise.

Any ideas?