Renpy (The thing i used to make the game) calls every version you create version 1. I just downloaded it from the game page and it has all the updates that should be in version 3.
Its that way since itch only replaces the old versions if the file name is the same, otherwise you'll have to delete the old files manually, losing all the stats on the old files and i want to keep those stats (hopefully all that makes sense)
and I'm happy you're liking it so far :D