The top lid (black trim section) actually curves inward slightly toward the center of the bed. I sanded mine to get rid of the highspot because i was running into the same issue.It popped up when I closed the box. It is like the seal they provided is too thick for the space there. When you close the box it prys against the seal and forced the rail up, I have a feeling it bent the middle mounting bracket some it will not go back down. Not sure if I am going to worry about it too much it moved maybe 1/8 of an inch in the middle.