There is definitely some confusion going on. “Wp-e-commerce Fedex Shipping Module” is not one of my plugins, and I’m pretty sure it was never intended to be used with “eShop Shipping Extension”.
My eShop shipping plugins are an extension of eShop for WordPress. That’s why you’re seeing that banner – you probably have WP e-Commerce installed, and not eShop.
I do offer a Fedex plugin in the link you mentioned, but it’s intended to work with the eShop Shipping suite.