The app will only return rates for products within the General Shipping Profile within Shopify. 

If an order only contains products from a Shipping Profile that isn't the General (Default) profile, the app will not return rates for those products. 

First check to see if you even have any additional shipping profiles configured. If you don't see any then you can skip this article. 

Go to Shopify Admin > Settings > Shipping 

Additional profiles are listed under the General Profile (Default)

Click Manage rates on an additional profile to open it and see what products are assigned to it. 

Then click Manage Products

Then start searching for a product in the search field, in the results it will list which Profile the product/variant belongs to. 

The app will only show rates for products marked In General shipping.  It will not show rates for products/variants that are in a different shipping profile. 

If you want to have the app show rates for those products, you must assign those products back into the General Shipping Profile.
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To remove the product from its profile, and return it to the General Profile, you can uncheck the box next to it. 

And then click Done and Save the profile.