Hi,
i can confirm what you describe - it's a bug.
A simple workaround for the moment is to set the Waypoint size (parameter wpradius) to 0 - the waypoints will (technically) still be on the map, but with a size of zero they will not show and will be "difficult" to be clicked
.
I'll try to fix this for the next release - thanks for pointing this out!
cheers, Frank