On Sale is calculating sales using the price before discount. I need it to use the price after any discounts.

The On Sale modules applies sales in the order set on the main Sale Overview page in your X-Cart admin section.

For sales based on subtotals such as a free shipping sale you will want to set the Order to apply to a number higher than any sales that are discounting products in the cart. This will then calculate the subtotal based sales on the discounted price.