The waypoints only fail if they were placed by a curator but they work fine if they were placed in Eden Editor.
Advanced Waypoints are located in configfile >> "cfgWaypoints" >> "A3". In contrast to the default waypoints they have a direct reference to a sqf script in their class definition.
Problem was also reported in forums: https://forums.bistudio.com/topic/189798-zeus-land-way-points-do-not-work/?hl=way-point