Exactly! You described my problem to a T !! Warped to the point of having approx 3/8" of space at the topcase seal at either end. They were obviously not "flapping in the wind", but I could envision an eventual lock failure and/or water leak problem in the future if I didn't do anything to solve...
I know a lot of us are frustrated with how loose & sloppy the Yamaha OEM topcase lid can be even when it's locked! I picked up a 2-pak of these "Spring Loaded Butterfly Twist Latch Keeper Toggle Clamp for Case Box" from Amazon, and they keep the lid closed nice & snug! They JUST fit !!