I had (have) the same problem with my '08 7 passenger Tribeca. It was driving me NUTS! A brand new vehicle that costs this much shouldn't have rattles like this (unless it's a GM product...ouch!).
I tried everything...took the tool box lid out, took the tool box out, rode with the third row seats up, hooked up all the seat belts in the 3rd row...but no matter what I tried, it continued to rattle.
I hear the same kind of squeaking you mention when slowly closing the gate. I was thinking it might be the struts rubbing a bit, but it doesn't appear to be. I'm not sure if it's temperature related, as I've only owned the car since mid October and it's been relatively cool / cold since then.
I took it to the dealer to have them look at it and they've ordered a replacment seat belt housing for the middle seat in the second row (goes in the ceiling). They also ordered a new interior panel for the rear gate.
Since having it in for service, I did some more testing and was able to resolve the problem by putting a folded towel on the driver side floor of the rear tailgate area, so that when the door closes, the towel is wedged between the bottom of the tailgate panel and the bottom sill of the gate area. It's not pretty, but it's worked and I can now drive my new vehicle without going batty.
I take it to the dealer on Monday to have the new parts installed, so I'll let you know how it goes.