I wonder if this is a problem at the product level... I'm thinking that if the fulfill button isn't showing on an order, it might mean the product has "this is a physical product" unchecked in the product page.
If fulfill is showing but then fulfill with amazon marketplace web button isn't showing, I would look into the product page as well to make sure it's still showing inventory managed by amazon marketplace web.
If neither of those work and you want some help, I can send a collaborator request to take a quick look for you to make sure everything is connected correctly (I do a lot of work with FBA and Shopify).
My best guess without seeing is it's a setting on the product level.
Founder of
Speed Boostr (Shopify optimization experts, theme customization, custom app development).
Creator of
Shopify Analyzer (first performance analysis tool for Shopify sites, free for the Shopify community).
Creator of
Order Automator (auto tag orders and customers + auto fulfill orders + email notifications).
Creator of
Theme Scientist (A/B testing app) and
Tip Jar (add a tip button to your store).
