What is “the project tab thing”? It’s strange, because as per the TMX changelog, the only changes to the map format have been the addition of two attributes and a custom property type, all of which should only affect the file when used. Maybe the game is checking the version? Did you check the files for any other difference?
Maybe you could open an issue about your problem at https://github.com/mapeditor/tiled/issues? This comments section isn’t really suitable for long threads.