I'm in exactly the same boat - playing Mictlan and currently trying to work out how blood sacrifice works. And trying to get another two player (both me) game to the point where I can see if 'enslaved' Theurg Communicants (via the spell Master Enslave, for example) could be used as troops (rather than commanders) who still have their built in slave matrix.
But that is another story.
What I have understood on the sacrifice front is that:
1) a priest can only sacrifice as many slaves as he has priest levels. +2 if he has a jade knife. (+1 if he is at a temple? I forget)
2) He will sacrifice as many slaves as he has in his inventory, up to his max limit. This is a way of letting you choose how many slaves he will sacrifice, if you want to ration your priests.
3) If he is in a province with a lab, he will try to replenish his stock of slaves from the lab's supply
4) each slave sacrificed acts like a 'normal' dominion's temple. Possibly more powerful, from the manual, but that might refer to the fact that you can sacrifice several slaves.
So I would guess that your priest was happily sacrificing away (they stay on 'sacrifice' until they run out of slaves) until the stock of slaves ran down, so he could only replenish one slave. It would be curious to see if, the next round, he replenished the full three slaves from the lab or stayed at sacrificing one slave a round (which would be my guess).