If you're using Windows Mobile based device, you may try checking/unchecking the "GPSID bug fix" option in Configuration > GPS Settings.
There has been a firmware bug concerning GPS immediate driver in some devices (e.g. from Mio). Since not all apps use the immediate driver, the error does not appear in all apps.
I had a similar problem during my last bicycle tour:
RunGPS showed 2980 km! (correct was about 29 km)
I uploaded the data to gpsies.com and downloaded it as kml file.
Then I saw the problem:
the last saved GPS coordinate was corrupt: lon was 48.x (which would be the correct lat value!) instead of 8.x degrees. SO that coordinate was totally out of range, leading to a big distance value added.
Maybe a bug in RunGPS?