The issue will be the base model shape. When making futa's there is a morph that turns the base male mesh shape into the base female one. As the female mesh is already that shape it will be the equivalent of setting that morph to 2 on the male when you try to add it to the female model. If you have used that morph, set it to zero on the male and bake the morph using Morphmerger, when you add it to the female it should look right.
I don't know if there is an equivalent morph for turning the base female to the base male shape. Maybe try setting the male one to -1?