I have heard repeated reports on http://mesh.openisp.ca/ that editing a page that has a waypoint in it will sometimes make that waypoint disappear from the main map. I have yet to understand why that happens or how, but multiple users have reported that.
A workaround is to rebuild the whole wiki, although sometimes re-editing the same page will bring the waypoint back on the map.
I have been able to reproduce this by simply creating a new node. It will not show up on the map until the wiki is rebuilt or the node is resaved. -- anarcat