Yeah, Itch doesn't allow funds either "donated" to a free project or spent on a file to count when you upload a new file with a higher price set for just that file. So many people use Itch to have the project at $0 and Itch won't change their system to reflect how people actually use it, because they intended the file pricing to be for DLC additions, not the main game file. Seen other devs make that mistake and lock purchasers out of content if they increase the price further on in development.
The current Summer Bundle did include the paid Windows version when I downloaded, so I'm guessing you made the final version the project file, and set the others to $0 individually?