Yesterday we stress tested it and located a posible reason why this is happening, if any of the players on the server goes to the nether while someone has a map open in the overworld, or the player in question is moving inside the nether, the chunks will not load correctly, in rare occasions it will happen while no one is in the nether but is moving using the minecarts on the tunnel, the tunnel has around 2000 blocks in length.
Yesterday we stress tested it and located a posible reason why this is happening, if any of the players on the server goes to the nether while someone has a map open in the overworld, or the player in question is moving inside the nether, the chunks will not load correctly, in rare occasions it will happen while no one is in the nether but is moving using the minecarts on the tunnel, the tunnel has around 2000 blocks in length.