I have the same problem (Shakala has had 111 children so far, always warriors). I noticed I was missing quests when I finished 3.41 and the quest numbers (from the walkthroughs) were off.
Causes of bug? I noticed that the goblin population seems to be capped at 100, and with Shakala, Sequoia and Obeah all popping at the same time (because I use enh. fert. potion to get all three pg on same day), maybe the "daughter" is eliminated by the population cap or because their are too many births at the same time?
I'ma try an kill off some goblins, and just get Shakala pregnant to see if I can avoid the bug.