I have a Garmin 60CSx which saves my flights one gpx file per day.
So one file may contain more than one flight track.
FlightTrack displays all the tracks well in the track list when I open the gpx file.
However I did not find a way to save each track as a separate IGC file, FlightTrack always seem to save the first track.
Thanks for your help.
I don't think there is a way to do it within FlightTrack. You can try GPSBabel to perform this conversion, else by selecting the track within the GPX file in a text editor.