Warped boxes are driving me nuts.
I thought that was the steering wheel sticking out of the pirates pants......
Seriously, I store my games the same way and I find the boxes that have their contents slid to the bottom and push out on the lid are the ones that may warp.
Tighten your boxes up; squish them together. Also keep some cardboard things that tokens are punched from to store in your box to keep the contents from sliding to the bottom of the box and pushing against the lid in such a concentrated fashion.