Thanks it wasn't the hand history location, that was correct. I think I have figured out what is causing this or at least a symptom of what's causing this. The stats are only not showing up if one specific player is at the table, sounds crazy but that explains why it was mostly high limit tables (he's a high limit player). If he joins the game late, I will have stats on the other players but once he plays a hand, they won't update anymore.
Is the solution still to create another database?