I'm not seeing that. I get both backup and the correct directory.
Are you sure it is working for tracks? It might be possible that it isn't working for both, but I don't think there is anything that is different between tracks vs. waypoints.
If you can double check that it isn't saving I will re-write the way it works in a more robust fashion. This was suppose to take care of losing data, not cause more of it!
Also, there was a bug in 2.77 that caused all tracks saved to LOSE time data! I'm putting out 2.78 with the fix right now and will send email.
Thanks for the beta testing.