Waypoints are assigned at the GPS antenna position ...
(You didn't mention where the GPS antenna is ...is it in the head unit or is it an external antenna ...??)
So your present GPS antenna position (in live navigating) is trying to get back to your previous GPS antenna position (when you marked it) ...
This is why one wants the GPS antenna as close to the xducer as possible - so that the GPS position (when marking structure) is in the same place as the Sonar information (under the xducer) ...
Rickie