I came across a player on my server whose waypoint regions had all been locked. Going to those regions would not unlock them. I first tried to unlock them via the command (/lotrWaypoints). However that returned an error message: PLAYERNAME already has the waypoint region SHIRE unlocked I then asked for a screenshot to prove that it was really a problem and the waypoints weren't toggled off or something. The player in question is near the Edoras waypoint in the screenshot. You can also see that the player has two custom waypoints in Rohan. I then downloaded the LOTR player data to see if it was correct and everything looked fine to me, but I've uploaded it so you can check it for yourself. Finally, I fixed the issue by using the command (/lotrWaypoints) to lock and unlock all regions that were supposed to be unlocked as indicated by the player data file.
The main reason I'm posting this is to see if others have had an issue like this and it is actually a bug, or if this is just a strange mishap.
I think I might of experienced this problem on TOS before, all of my player data excluding inventory and if I remember correctly alignment was gone, Mevans checked and the data was perfectly fine, when the server restarted it was fixed, no idea if this is the problem they are having though
Now that I think about it, I think my issue may have been caused by the player playing on another server or singleplayer before playing on my server and without relaunching minecraft. Waypoints have been known to show incorrectly after playing in another world.