I kinda read that as the OP thinks the rear hatch was replaced because the key doesn't work or that he thinks that when it was replaced the old cylinder wasn't swapped because the key didn't work, thus my recommendation to try a fresh key before he goes any further.
When I bought my truck from a little dealership the keys would not unlock the door at all. Not knowing this, when I finished the test drive I locked the doors and handed the key back to the salesman. He started freaking out because they never locked the doors, he explained. Because the keys don't work in the doors. I negotiated the price down further citing the cost of having the whole car rekeyed. They called a locksmith to open the doors so I could drive it home.
Turned out that since the only tumbler that routinely received the key was the ignition so these two wore in together where the doors were rarely opened with the key inserted in lock, and didn't wear with the key. As the key wore the still newish door locks no longer accepted the worn key. I had a new key cut at the dealership and voila all the locks worked off of that single key. Cost $8 IIRC.