How is this possible??

[Northern lights]

I'm planning to do a frame off this winter but before I pull this thing apart, I need to figure out why the box isn't sitting right. The drivers side is good but the pass side, the box is touching the cab at the bottom. The gap between the front of the box and back of cab is exactly 1 inch all the way across and the box-cab fit is good at the top but deviates at the bottom only on the one side. I've taken measurements all over this thing, front to back and underneath but can't find the cause. Thoughts??