This issue has just appeared for me with the latest version of GPSBabel (1.2.4_beta09202004).
 
Running the following command line results in a crash:
 
    gpsbabel -i gpx -f Input.gpx -o mapsource -F Output.mps
 
This is merely a small annoyance at this time as the output file seems to be correctly generated, but I thought I should let you know of the issue.
 
Thanks,
 
Jon