Something that strikes me as odd is that the breath test was done in June 2014 and the criminal complaint was filed earlier this week, a year and a half later.
I've known of several cases where a pilot was 'allowed to retire' after a positive drug or alcohol test. It avoids the negative publicity of a trial, gets the offender out of the cockpit and in the past seemed to close the matter with the feds. Sadly, some folks never conquer their demons and pass away soon after leaving the airline from what I've seen.
The criminal complaint indicates that the alcohol test was indeed random and that neither the tester nor the other crewmembers said they smelled alcohol on Captain Arntson's breath.