Yip, tracklogs containing files with trkseg parts just gets dumped into a single file, but I've found it useful having the trkseg parts in the file because I may end up breaking a tracklog into two if, for example, I've taken a ferry. Sometimes there's bit elevation spikes and when the Garmin has been switched off for a while and it's also nice being able to remove the inconsistencies.
Anyway, problem now kinda solved. I've discovered the tracklog will contain all trkseg parts after the file has been automatically achieved by my Etrex 20. Grab the "Current" file, no trkseg. Grab the archived file and the file contains trkseg components. It's a bit odd, but there you go.