Board Thread:Bug Reports/@comment-26240225-20150714010310/@comment-25101089-20150714133531

Was this world from before Beta 23? Because if so, the waypoint duplication bug would have built up then, and all the duplicated WPs would still be saved even after the cause was fixed. It just wouldn't duplicate any more.

Open your player data in the LOTR folder inside the world folder with NBTExplorer (just google it and download). Look for the list of custom waypoints. Are there lots and lots of identical ones? If so, delete them all (except for one). Then, reload the game, and see if the bug is fixed. If my hypothesis is correct it should be. Otherwise it looks like I didn't fix the bug after all, but since I've not heard any more about this since beta 23, I think my idea is probably right.