Mercado Libre's two shipping types behave differently in Escalafy.
Full shipping
It's pulled automatically. There's nothing to configure.
Flex shipping
It has to be configured manually in the Shipping section, with a custom cost.
Shipping discounts
We also pull Mercado Libre's shipping discounts, including Flex ones. You can see them in Latest orders: they show up as a positive balance inside shipping costs, order by order.
If a Flex order shows zero shipping, it almost always means the custom cost hasn't been entered yet, or it was entered and not reprocessed.