I've had problem with Lara pregnancy and stoping her from taking pills. By checking forum I didn't find any solution, beside of spamming training with her. Tried ~20 times, but didn't work. What worked? Doggystyle after inviting her to MC room. Maybe there's something more required, but tried 2 new saves on skip before this, everything according to walkthrough and since I was repeating game, I didn't bother in any extra scenes, so I'm sure this doggystyle was first time.
Edit: You may also try starting with 0dex, so you have 5 at the end as her new event gives you +1. I don't think it should matter, but who knows. If you have more and don't want to start again, just use "stats.dex=5" in console.