Freight update depends on a previous configuration of logistics that complies with the commercial policy vinculated to the marketplace. That required configuration follows the same logistics standards of the store. However, first you must associate the commercial policy, vinculated to the marketplace, to the Dock section.
After these steps, you must wait for the update, which can take a few minutes.
If the commercial policy chosen already has its own logistics set, the following steps are not required. You just need to index the products.
In some marketplaces, you can configure your system so that the freight values used in the purchase are those settled by the marketplace, and not by the seller (your store).
If you want that, you need to configure the logistics of the product to be attached to the right commercial policy and, in addition, to set a free shipping sale for this policy.
This way, freight can be calculated without conflicts with the seller options.