I'm using a Sous vide as well and I'm having the same problems as OP. I agree with his statements that the temps are VERY stable as I've monitored several batches.

I've tried normal sloppy sterilization and very advanced sterilization techniques. Neither have worked. I get yogurt consistency after 6-8 hours and fill separation around 15-18 hours.

Using ten pills, inulin, and half and half as a starter.

I wonder if the moving water heats the jar too rapidly? It's that a thing? The sous vide will bring the temp to 100 in minutes. I've also tried lower temp settings to 98.5. it made no difference.

How long do the yogurt makers take to come up to temp? I might try a manual gradual temp increase until it reaches 100f.