When you modify a scoreboard and then exit the world, and then enter the world again, the scoreboards are not saved and it uses the previous session of scoreboards (from when it last saved).
This is a world which was generated in an earlier version of the game (1.12 I believe) and then opened in the latest snapshot and used with scoreboards.
I have the same issue. Even after resetting the save data and creating a new one didn't resolve the issue. Changing, deleting and adding scoreboards will not save. Also when using '/save-all' and then restarting didn't work.
Just adding some information about the things I've tried. And letting people know you are not alone on this. Hope this will be fixed soon! :3