GPSBabel 1.3.5 was released a few days ago, and for those of you using the popular NaviGPS units I am pleased to be able to say that the new release of GPSBabel includes native support for the NaviGPS.
This includes both direct access to stored tracks, routes and waypoints via the USB cable as well as the ability to decode waypoints and tracks copied to the SD card if you are using a recent release of the NaviGPS firmware that supports that.
The code has been tested with my GT-11 unit but should work with the BGT-11 as well, and will hopefully work with the new GT-31 and BGT-31 units when they arrive - please let me know if you manage to test with one of those.
The name for the new driver is "navilink", so to recover waypoints over the USB cable on linux you would do something like:
gpsbabel -w -f navilink -i /dev/ttyUSB0 -F gpx -o waypoints.gpx
Any problems, give me a shout...