The reason that the Auto Mark Rules does work could be:

  1. Having the same Personal Location Name in multiple places
  2. Having the same GPS co-ordinate location with multiple Personal Location Names
  3. When an automark rule is set up you would select the "apply in reverse" button so that the rule applies in both directions.
  •  If you set up a rule that from home to office is an private trip and download your data it will automatically mark this as such.  
  •  If you then set up a rule that from office to home and in reverse is always a private trip you will have duplicated the rule.