Edit: I didn't realize that I was posting in 5th Gen. I have an '06 t4r. Part # is probably different.
I had this problem and was happily surprised to realize that the lift gate window wasn't shut entirely, but my happiness faded when I then noticed that it didn't go back up evenly, so I need a new regulator. Don't let people close the hatch without instructions - they will invariably slam it shut. (I always try not to sound like a pretentious douche when I say it.) I knew the gentle securing of the automatic close/lock feature with the hatch was put there for a reason and I finally understand why, I think.
OEM regulator for the window is Toyota part # 69807-35020. Retail is around $120, w/o motor.
Sent from my SM-G950U using Tapatalk