Hm, weird. I wondered whether you had hundreds and hundreds, which might explain some strange behaviour. If you're happy to, would you be able to upload a copy of your prison to World Of Wardens and then let me know the name? That way I can download your game, which makes reproducing the issue easier.
In the mean time, I'd recommend saving your prison to a new save slot, just on the off-chance that fixes it.
Nat D11
edit: there's no reason that the cells should affect your intake at all as far as I'm aware!