Is there a mod/repair for OEM tonneau cover?

Third this. When I got mine, the standoffs on the tonneau were hitting square on the rear tie downs. Moved the tie downs aft 2" and haven't had a problem since

 

I'm having the same problem. I will have to try some of these tips when I get off work later. Thanks everyone

 

Make sure if you have the cleats in they are not obstructing the latches or the "legs". I had an issue with mine as well until I noticed the cleats were in a position that wouldn't allow the cover to fully latch shut. Moved them a little bit and problem solved.

 

I had the same problem on my 2016 TRD Sport Double Cab stock tonneau. There was a gap at the very front edge and over the tailgate. I was able to fix the gap issues and adjust the latches to get the “double click”. Here is what I did; hopefully it will work for you too.

1. For the front lip of the tonneau I removed the spacers under the latches. I was still able to open and close the latches without any issues. When I pushed down hard on the side with the locking latch I heard both clicks and it was seated flush against the bed.
2. For the part over the tailgate, I found that I had a tie-down bumping up against the rubber foot on the tonneau. I moved that and it sat slightly tighter over the tailgate. To make it flush, I tried removing the spacers under both latches. Unfortunately, after tightening the bolts the latch was squeezed against the underside of the tonneau. I could unlock the latch, but the spring wouldn’t be able to reset it to its open position so I had to put the spacers back. I kept adjusting the placement of the latch (forward,backward, sideways) and tested closing it each time. Eventually I had both latches positioned where I could press hard on the tonneau and hear both clicks. It now sits flush over the entire bed.

 

Ok resurrecting an old thread here but wanted to say thanks, this saved me some trouble. Just got my truck w/ tonneau last week. The salesman demonstrated the first "click" on the back lid but it was still a little funky looking.

Finally got around to poking at it this afternoon and, lo and behold, there's a second, much quieter click that happens if I push down a little more, closer to the hinge / latch. Now it sits nearly level and seems more secure. Seems like my cover is set up correctly, though it takes a bit of finesse to get it all the way latched.