I d don't understand since I stuck with the same version during the whole save
I assume that you have replaced files between versions. What you have to do is delete the game and download it again. This has to be done with all versions, delete the old one and put the new one in the same place. You can replace files but you risk getting bugs and possibly have more bugs than are actually fixed.
NOTE: Always make a copy of the saves folder (it's inside the game folder) just in case, although it shouldn't be necessary.
I just downloaded the game to make sure and you are both right. Something strange would happen with Itch when uploading it because the rest of the sites where the game is published work correctly and being a compressed version has nothing to do with it because I do it after publishing the normal one in the rest of the sites...