Both me and another Connect user that I've been speaking to have had the same issue when using Connect (completely separately, but same symptoms).
When putting in a new course, and then saving, for some reason the start and finish points swap places (they are distinctly separate by some distance).
Secondly, if the lock/unlock state is changed, this error appears:
You don't have permission to access "connect.garmin.com/.../minroute.faces" on this server.
Reference #18.278e7b5c.1489044930.e579d2
Thirdly, when returning to desktop, then jumping back into courses, all courses don't appear until the order is changed, then they all appear.
Very odd behaviour. Not something I've seen before.