Is the rubber glued into the top leading edge of the daggerboard trunk? If so, then that is probably the culprit. Check the fit with the boat on the trailer and the boards in the fully down position. If there is a small gap between the very front edge of the dagger board and your rubber spacer, then it is likely that the rubber is too thick or extends too far aft, and the board is getting wedged in against the rubber. You would need to trim back the rubber or use something more forgiving instead like carpet. When it comes to padding the daggerboard trunk, less is more. Definitely better to be on the "sloppy" side.
Also, as others have noted, if you don't pull the board up properly, it will wedge into the trunk.
Make sure everything is running smoothly on land before hitting the water.