I have just done a blog post about how to use these in the simplest way. There are loads of sites about setting them up but I always got confused which files to use when transferring the data.
I hope this helps others with the same problem
www.redsurfbus.com/2011/03/using-navi-gt-31-speed-genie-gps-for.html
This is the best and only wayhttp://mtbest.net/setting-up-navi-GT31.htm
After that I just load file after session, delete all from GT and ready for new one
BEST FILE FOR USE IS *.SBP (sbn, bin), never gpx
This is I think Binary File that contains many parameters for calculation)
I use only GPS RESULTS of Manfred Fuchs, software is validated for GPSSS
Like I say in the article, Tom's site that you have linked to is the best for settings, if a little technical for some people (I have set up several for people who cannot follow the instructions).
I just wanted to give a simple few steps to using it - i.e making sure they use the SBN file and not the others that you can download off the unit. Some other GT31 users at my local spot said they found it really hard to get data off the system - because they used navilink and transferred the gpx/nmea files rather than the easy way.
Also - The unit will not update when using VISTA or WINDOWS 7 but does so easily in XP. These are just my findings, and have tried several times with newer PC's, always having to dig out an old XP machine to do the job.
also use xp sp3
for vista and w7, first YOU MUST dload new drivers from locosys site, and new navilink II
that two thing is important for vista and w7
in every new tom's firmware new updater )0.71) is included in zip files, and this ver.works under w7 and vista :
GT-31 USB Driver Only for Microsoft Windows 98/ME/2000/XP/Vista/Win7http://www.locosystech.com/download/driver/PL-2303_DriverInstaller_v130.zip
GT-31/BGT-31 Utility NAViLink II 98/ME/2000/XP/Vista/Win7
www.locosystech.com/download/handheld/GT-31/NAVILINK_Installer_V250_B0826A.zip
and new updater is in zip from latest tom chalko's firmware on his site
Well that's the first time I've seen it stated "they won't update using Windows 7", so is that why I've spent many hours trying to upload the latest software to no avail each time? I always get the error message just at the last minute! 
