I just looked under mine.There is two rubber pads,one on each side.They are at the very most rear of the bed to frame.I noticed that my two outer wood planks are very close to the frame where it arches.Could your wood be popping against the frame ?
I've got a 2003 silverado that has similar noises,the dealership says it's normal.I think they have too much lash in the rearends.

1951 3100 Chevrolet
1951 Chevrolet Suburban Carryall
Image
"A house is built with boards and beams. A home is built with love and dreams."
"Look deep before you leap !!!" / "Everything is Everything"
"If I say a mouse can pull a house, hitch him up"