Yes, I can see that. It doesn’t make sense to me. I am not able to recreate it either.
First, let’s get the basics out of the way — did you set the variation prices after you set the markup on the attributes? Or, is it possible that you added the plugin to an existing site, set the markup on the attributes, but did not set the variation prices after that? Markup by Attribute hooks into the variation set and change price routines. So if variations with prices already exist, you have to go back and set the same price on the variations in order to calculate the new price. (I know it’s a pain when you have a lot of products, but I couldn’t make it do this automatically).
If that’s not the issue, then can you tell me what level of WordPress you are at? Also, is it possible to send a cropped screenshot of the admin page showing one of the product variations? I’d like to see the variation price and the description fields.
(Thanks for the compliment, by the way. But it doesn’t do you any good if we can’t make it work!)