This is a known issue and one I am trying to clear up. I do not understand why the Garmin protocol is not behaving as a USB device is supposed to.
What happens is that the transfer completes but when we check how many trackpoints the track is supposed to have it is significantly lost -- we haven't been able to figure out why but have noticed the same problem in other GPS apps. However, mapsource works 100% so there is a fix, we just haven't found it.
Hopefully we'll get it soon, but thanks for reporting the bug.
Unfortunately both of the authors have been out of town and things occasionally slip through. I could have sworn I replied to the email, but I see there was someone else with the same issue -- on a VistaC.