(Some) Subfolders not being linked in Graph View

[lambjc]

I've ran into an issue where some items linked by waypoints aren't having the links generated in graph view:

All the yellow dots (and there's some green and red scatted in there) surrounding the perimeter are linked using a waypoint file in their respective folders. However, despite a number of other waypoints appearing and linking out in the graph view, these one's aren't for some reason.