This might be a permission level thing. Do you have Run Game As Admin checked? That might be worth trying.
Also the confusion between the versions may be a sync issue with GitHub, which is hosting the mod. I've noticed if I update an XML file, it can take a few minutes before people see the change. Even going between regular view, and Raw view, it can be different. Something to do with caching. So it's possible, I think, that the configuration file gets updated and says "New Version!" but the installer hasn't synced up properly.