When we go out I have mine and my wifes board in the same rack, and my board is a bit bigger than hers and when we are flying across the lake, the difference of size makes my wifes board move around and unstable. Anyone else have this problem? the bungess dont touch her board

Put it on the other side. I don't have that problem because I have two seperate straps for each board on each rack.

what if you have only 1 rack?

Try stuffing a towel in there, maybe a cut piece of a funoodle?