If the gen2 tonneau covers are like the gen1 tonneau covers, the problem is likely in the cable pull mechanism attached to the bottom of the lock cylinder.
The gen1 covers had a very flimsy plastic hook about as thick as a fingernail. If the tip of that hook chipped off it would no longer pull on the cables to release the latches.
The deceptive part is that once you open the cover, the latch is released, and there is not resistants on the cables. The hook can easily pull the cables and move the latch release.
If you push the latch closed while the tonneau cover is opened and then try to use your key, you will probably see that the cables are not moving the latch release lever.
That's how I determined that the cable pull mechanism attached to the bottom of the lock cylinder was the problem. When I disassembled it to see what was wrong, I found the cheap little plastic hook with about 1/16" of the tip broken off and could not fully engage the barrel that turns to pull on the cables.
....Rich