If the *female* determines the gender, the only way I can see a *male* snake throwing *male* babies is if male bananas are actually actually ZZW, rather like how male calico cats are XXY. But, then, the male bananas should be mostly sterile, so that doesn't work either.
Other option, the female chromosome is often incompatible with the banana-carrying genome, causing failure to develop, along the lines of the fabled 'super spider'?
*flails* this is really strange and really doesn't make sense.