The user waypoint should end up in the exact position of the mouse cursor when you right-click; is this not happening?
We changed the user waypoint storage medium in this version. They're all stored in your My Documents folder under SkyAngel now, in a simple XML file so it's easy to share/edit/transfer/backup all of them without worrying that a future version might not find them (as has occurred here). Previously they were stored alongside the software's general settings.