I'm using a Garmin eTrex Vista C with USB. After downloading (follow download in map, add tracks to logbook) the track & viewing it on the map (everything OK), I disconnected the GPS & went away from the computer. When I came back (screensaver, password protected), the previous track was still displayed (highlighted actually). I now had a new track to download, but Topofusion wouldn't communicate with the GPS, so I had to close & restart TF. After doing this, I was able to download the new track just fine. I save my GPX files using the date only (as in xx-xx-xxxx.gpx). The new track was for a hike & the previous track was for a mountain bike ride. I use different directories for each file, but they had the same date (same filename). Next I wanted to look at the climbing data for each file but I found that my previous GPX file was not in the list of open files! I believe it was missing when I restarted TF as well, but I didn't look for it until after downloading the current track. I looked in the "biking" directory & the file was not there! The hiking GPX file was in the hiking directory as it should have been, but the biking GPX file was gone - as though it was never written to disk or was wiped off the face of the planet when TF saved the hiking file. My default directory in TF is the biking directory. My TF logbook shows the complete entry for the missing biking file, but can't load the file since it doesn't exist. I've had this happen at least 2 times now, each time losing valuable track data.
I really don't think I did this by accident but unfortunately I can't reproduce it at will. I really think it is an obscure bug in TF that is somehow related to the USB connection troubles and/or some sort of logbook & filename issue. I don't recall ever having this problem with my serial Garmin although similar loss of communication troubles did occur occassionally. There seems to be some trouble with the Garmin GPS when communicating & a loss of GPS signal occurs with either serial or USB, although less often with USB. There is definitely an issue with sharing the USB driver in TF because I always have problems if I have MapSource & TF running at the same time. I can run ExpertGPS & MapSource together without troubles. My guess is that there are driver resources that aren't being locked/unlocked properly. I have no idea if this is also related to the file loss issue though.
I'll try to watch for this again but I'm a bit paranoid about losing my data now, so I'll probably be sure my previous file is always safely on disk before downloading another just out of habit from now on. If there is anything specific I could test to help track this down, I'd be happy to do so.