BaseCamp 3.01 was giving me a communication error with my Dakota 20, and only downloading a few of my waypoints. I discovered that the missing ones in a file on the GPS, and importing it gave:
"/Volumes/GARMIN/Garmin/GPX/MBC_Wpts.GPX" is not a valid GPX file and could not be opened."
By experimentation, I found out that MapSource declared any waypoints where I had used the GPS feature to position average were thought to be invalid. the XML file for these contains:
<extensions>
<gpxx:WaypointExtension xmlns:gpxx="www.garmin.com/.../gpxx:Samples>
It's the <gpxx:Samples> key that seems to throw it off.