Funny you bring this topic up.
During our 4 week trip last August, our 6 year old rig developed some over-head noises/squeeks/rattles/banging, whatever best described it. I called the manufacture of our motor home to ask what might be the reason and if there is a resolution. The owner at Phoenix USA wanted me to bring the rig to the factory so they could take care of it for me. I didn't want to take a day off work so I asked if it was something I could handle myself. He said "sure".
Doing this completely eliminated the noise.
Our Overhead Cabinetry
Tools Used
Screw Overhead Cabinet Floors To Ford Steel Roof
For Reference, Ford Roof Prior To Assembly
Basically I fastened the steel roof to the cabinet floor, either so the steel would stop flopping around, or the cabinet got anchored better, or maybe both. Either way it solved all my noise problem up top.
If you have a bed up top instead of cabinetry, you might consider the same with your mattress platform. Just add screws every 6" or so around the pass-thru opening. Be sure to first drill a pilot hole and drop a coat hanger down to make sure you'll tap into the Ford roof.
As hotbyte said, if you have screws there already, maybe you only need to tighten them.