Checkout and cart calculations order

Testing out this plugin but finding an issue with the checkout and cart process. We have some custom calculations and are using a wallet system (terra wallet) as a points system. Users can redeem their points against items and bill their credit card if they don’t have enough points. This is complicated in the woocommerce system since a change in address can change shipping and/or taxes calculations so the checkout is always recalculating. When “Logged In As” a user our custom checkout process is not followed. I’m guessing this is a timing issue and something gets bypassed when using this plugin. Any suggestions?