Sounds like something might be out of adjustment.

I'd probably start by having the top halfway up (or down if you prefer, just so long as the tonneau cover is in it's vertical position) and checking all the hardware for anything loose.


EDIT: I just went out and looked at mine........ I have no noticable wear on any parts of the latching mechanism, I'd probably start with that. If you see any place where there's a wear pattern start checking there for something out of adjustment or possibly loose.