Hi menion.
Here is an NMEA-File of a track, which had half the error.

That means, that the track did not completely stop but lost a lot of points with available positions.
I added a screenshot of the track with manually added hints.
Short description:
1.) This is where I switched on GPS and got the fix with accuracy of 5 m. Then I switched the screen off and started biking.
2.) Here I made a short stop to have a look. So I switched on the screen, looked (track looked o.k.), and switched the screen off again. This in the recorded track is point no. 14. I went on biking.
You can see that from then on one more point is recorded, before a lot of points is missing although the position probably was available (from my experience with my track in the car, I described above). I followed the street "Am Kesselberg".
3.) Here locus wrote a position again. This happens if you are lucky. When I went by car, it often didn't. Instead no more point was written for an long time (more than a minute), so I had to force locus to write by pressing pause and record again. Maybe that locus would have started writing again after a few minutes, but that of course is not satisfying...
The points are numbered correctly within the track, that means the stop (2) was at point 14, then number 15 was recorded and the first recorded point after the missing positions has the number 16. By the way: within the part of the track, where the points are missing, my velocity was the highest, for it's going down a hill...
The parameters were the following:
Track recording: Intervall 1m, 3s
GPS: refresh 2s
So, although this is only half the error, I hope this will help you to find the problem.
Thank you for your help!
[attachment=0:2ldzy2jh]menion_track.jpg[/attachment:2ldzy2jh]