I've see that behavior from the game when there was a major disagreement between scripts (usually when I made a mistake while tinkering with them). In your case, I know I sound like a broken record, but I'd try a clean install first b/c that's nearly always the problem when people experience game breaking bugs with my version. Follow the instructions on the original post above for the install to the letter and not a step more and let me know if you get errors or it works please.
I don't think my tweaks would cause that and I have played female/futa MC's with several births without noticing that (though I usually tend to keep them pregnant as often as I can, since they don't become unavailable after giving birth like npcs). It used to be in Aric's 9.6 with pregnancy accelerated that perpetual preg could happen to any female/futa b/c sperm life could exceed the pregnancy period, but I believe it was fixed (still possible to mess it up by playing with the constants though in the scripts). If you try to accelerate to have them give birth immediately, it will break the game easily (don't know if that's your issue), so I always accelerate to 3 days and things work fine for me. Does any of that help? I'd rather not try to mod a workaround if your issue can be solved without it.