What version was the last stable version for you?
I'm not sure pregnant bellies during sex did ever always work or what the difference is since I toggled them of then again.
Well 20120402 keeps the bellies during sex but I noticed during birth, the only difference between 20120402 and the latest version, the torso and legs vanish half way through the animation with 20120402 but with the latest, the minute the animation starts the torso and legs vanish. I also noticed that if the player has "heavy tits" during the animation, the tits remain visible and only the belly and legs vanish. The last version to retain the entire body throughout the animation, for me at least, was the version when you first implemented the animation and it didn't have a timer. After that version of pregnancy, I deleted the game until yesterday when I figured I'd play with some of the updated mods.
The weird thing is, last night while using 20120402, the character got knocked up by a super mutant involved in that newer quest User29 added and that birthing animation played totally fine, no vanishing body whatsoever. But it was only a stage 3 pregnancy, this vanishing body thing seems to happen when its a stage 5 or higher pregnancy. Speaking of which, I noticed there's a stage 7 or 8 pregnancy morph now (or maybe it was there before and my pc just never reached that stage) but the skin texture is a dark brown while the hands and face retain the pc's original color.