Oh okay, I'm not sure if the updates work directly through the app yet. 

Currently the updates are uploaded as new files, rather than updates to 1 existing file, so I figure that may throw something off app-wise. This was for various reasons, but lately I am looking into integrating with the itch app, and hopefully have that integration ready by the next update.

Until then, I recommend trying to download directly from the browser and please let me know if the same issue occurs that way.