From what I can tell, changing the daughters relation isn't the issue as it just changes what you call the daughter. The stepmom vs mom variable changes when you change the relationship of the MC from stepdad to something else. There are 4 choices and if you don't pick one, it puts the mom to default, which makes her stepmom. The choices are: uncle/aunt, Master/Mistress, Father/Mother and father/mother. So if you are lazy like me and just deleted the "step" from "stepdad" you end up not picking one of the choices and get the default "stepmom"
TLDR: Don't put "dad" as the MC relationship, put "father" or "Father".