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I have had this problem since buying my car and it was driving me crazy. I took it into the dealership and nothing was fixed. Last night, however, I followed the advice of someone on another thread and put two felt pads over the stoppers on each side of the top hatch, and electrical tape over each of the latches (2 on body where bottom hatch connects, one in middle), maybe 3 layers deep. Today I have not heard a single noise and it is totally fixed. Try it and I think your problem will be solved.