Somehow, shipping rates are not applied to the total when checking out and paying. It does show when selecting the shipping method, but not on the final order review and is not submitted as part of the payment.
The way it's set up is essentially a single shipping method, with geographical rules/zones. There's a "General" category, which is the default, and then an "Accessories" category which applies to smaller items related to that category. In the shipping method's various rules there's a different price set for the two shipping categories, and the non-default "Accessories" category is not being applied.
I'm assuming/hoping it's a user-error on my part, and curious if anyone has run into this, and know of a fix?