The tonneau cover center hinge seals where different from 2001 to 2002. You may have a 2001 tonneau cover that had little plastic diverters that fit under the cover at the outter edges of the hinge and directed any water that leaked past the outside edges of the hinge seal to drain out over the bed rails. These little gutters/diverters were just a small strip of plastic about 2 inches long and about 1/2 inch wide would easily became disloged, fell out and where thrown out or lost. If they were found laying in the truck bed, most people did not know what they were or where they came from, and got thrown out.
Another thing that some people forget is that when you open the cover, the water will run down to the center hinge and leak into the bed at the outside edges of the hinge. So it's possible that you cover is not leaking but opening a wet cover lets the water in. To check that use a flashlight and open the tailgate to see if water leaked in before opening the tonneau cover.
...Rich