I have WA 3.7.2.1 and also the same happens with WWP. I'm sure this is a known behavior of the game, but to me it's a bug.
If you use a custom scheme, or even if you change one single option in a regular scheme such as intermediate, the tools in your ammo such as low gravity, select worm and jetpack are lost. Is there any way to make a scheme chosing the number of tools available, or modify the regular scheme without losing them?