The ability to keep WooHoo and TFB separate is if you care to have the base game mechanics untouched. WooHoo is just for fun, and if that's what you want, that's what you get. Otherwise, both are merged, giving birth control a little more purpose.
As for the 0% pregnancy, I've ran a few tests and ended up releasing the v2 version. It doesn't actually address anything in this regard though, as pregnancy chances were working as intended.
It's hard to say anything more, I didn't see what you did in your game to have a suspicion of anything. Menstrual Cycle chances change from day to day, as the cycle progresses, but I have to assume you know that and you know that the pregnancy chance could increase.
If you have anything more to say about this, perhaps you did more tests and you found out something or it's related to some external element, please let me know.