From Ser on the forums:
Checkout the screenshot. The subject is the pink radar. I was flying straight towards it (white cross) and then edited it and set a new location. Now it's shown as inactive in the list but navigation is still visible on the navball and points towards the old position. That's until I reactivate navigation manually.
I guess the root of the problem is that the NavWaypoint is not updated when custom WP's position is edited. IsNavPoint() returns false because the positions do not match, that's why it's not checked in the list but in fact stock navigation is active and still set to the old location.
From Ser on the forums: