I've spent a considerable amount of time trying to find about this issue. The lock that the back glas latches to doesn't latch. There is a cable from the lock to an (actuator?) inside the tailgate. I'm guessing my problem is that aforementioned cable has too much slack. Seems like the metal canister with wire is supposed to hold the wire tight. It doesn't, just seen the post about using tape on the glass part to stop the god awful squeaking that will seriously cause me to hurt someone. But I live in memphis so the need to have a locking back glass is rather important.

 

Yeah Mine squeaks like a SOB too. But sounds like it might just be stuck try spraying motorKote or WD40 and try to turn it with the key. But not sure how to fix it but here is a diagram of the gate

 

when mine didint close i found that a tiny spring was the culprit that was keeping it from closing i fixed the small spring and baam no more flappin window.

 

check the adjustment on the latch itself (10mm bolts) by moving it up, I got my actuator working as suggested above, the cable will be lose, but found the vertical lever that the cable was attached to was bent changing the throw of the movement (took several adjustments to figure out where it needed to be), you can also check the latch by useing a screw driver as the stricker it should be two clicks- fixed mine when I changed the lock cylinder and brought new life to the truck nice option to have