I doubt the mod creator will do anything about this, but if anyone might have some insight on the problem that would be nice.

So I don't know why, but when I right click on waystones it no longer properly saves any waystones I activate, Natural or Manually placed.

When I right click a waystone, it'll show as activated, and will appear on my teleport list for waystones, however if I attempt to teleport to one, it will say that the waystone no longer exists or was moved, also apparently I can get the same waystone activated multiple times and have it show up on the list multiple times, attempting to teleport to any of them causes the one selected to state the same message as before, if all bugged waypoints are removed from the list then the waystone with the same name will appear inactive again.

I'm guessing it's a mod conflict, what mods are known incompatible with waystones?

Found the culprit mod. Don't use the 1.12.2 farlands mod with this one, it causes the problem stated above.
Gonna close this.