HypersomniacLive: It's possible that it's an error on GOG's side when shuffling the games in the Flash Deals. In the case of
The Banner Saga it took the place of a game that was discounted by 50% in the previous round. Could also have been the case for
Heroes of Annihilated Empires, and if you remember this did also happen in the Fall Sale (can't recall with which game though).
Heroes of Annihilated Empires was the game from the Fall Sale that replaced Deus Ex GOTY which had 75% off. Anyway, this whole discount mess is more than likely a bug, which also made an appearance on the Mount & Blade bundle as well, which was supposed to have a total discount of 75%, but both With Fire and Sword and Napoleonic Wars ended up having a discount of 1% less and costing each 10 cents more.