I was hearing something from the back in my 01 X5 and I took some of the fuzzy part of 1/2 inch velcor and put it around the parts of the latch on the upper door. It is kind of V shaped and it slides into the bottom door latch...this keeps it tighter. you can also put some fuzzy stuff on the little rubber stops on each side. You have to slam the top door harder to get it to shut but it gets a tighter fit and it stopped the noise on mine.

Can you see any spot where the top door hits the bottom door. I had a little line where the paint was worn because they were hitting. I adjusted the rubber stop out a little as well as adding some of the fuzzy part of the velcor....look for the rub. If you have it adjust the rubber stop out a turn or 2.

I thought it was the spare tire and I put foam around all of the tools but it didn't seem to help....but you might check if the velcro doesn't work...

Good luck!