File type detection briefly inspects the data to guess what game/language it belongs to. Seems it passed the English Crystal heuristic and was therefore assumed as such.
Does this still happen if you save in a different map, after changing boxes to another box in game?
If that isn't a valid workaround, I can possibly add a branch of code where if it passes both, then it checks the checksums too, but that would be a compromise that impacts manually edited files to no longer being recognizable (if they also end up clashing) hence maybe needing a more detailed detection heuristic.