Given your configuration of enabling the loyalty points program but setting the earned points to zero I can see that causing unexpected results. I'm guessing this is happening as you're capturing the payments (probably via shipping) of orders that were placed before the points change. I would not expect this to happen with orders that have already been fully processed (i.e. paid, shipped, complete), except if you edit old orders that were placed during this period of 0 earned points.

Orders placed during the time when you had the loyalty points program enabled and the earned points set to zero, will earn points at the current earned points amount when the order is marked paid or the order is edited.