Re: Rear window / Tailgate issue / Grrr!
My Jeep developed a similar issue. It's not identical to the other liftgate alignment problems here, but it's in the same vein. I think heat expansion might have pushed the upper-right corner into the D-pillar.
My jeep had been parked in the sun all afternoon. I lifted the liftgate and as it neared fully-open, I heard a clunking noise. I closed and re-opened a few times to try to pinpoint the noise. It happened each time I opened it. It turns out the upper-right corner of the liftgate/spoiler sits right up against the top of the D-pillar. The paint has been scraped off of both the liftgate/spoiler and the D-pillar. Bare metal is showing on the D-pillar.
After it cooled down outside and the Jeep sat in the shade for a while, the problem stopped happening. When cool, there is about 5/32" of clearance between the liftgate and the D-pillar on the left side, but no clearance at all on the right side. It looks like the gate always rubs the pillar, but when it bakes in the sun that tiny bit of expansion really pushes the parts together.
I'll be taking it to a dealer, but I figured I'd post here to add to the issues already reported.