Please ALWAYS clarify the precise, exact scenery used AND if you used a GSX profile and if you do, the precise exact link to where the profile can be found.
This problem looks like a scenery ground elevation issues and/or possibly the GSX profile with waypoints placed in places where the scenery has either an elevation change or just a crash box, which causes the waypoint to be raised, even if it's set on ground, because "ground" there is not at 0, due to the crashbox of the object, for example a terminal so, basically, walking waypoints shouldn't be placed inside terminals, if terminals have been compiled with the crash box enabled.
