These boarding passes all originated from a single American Airlines ticket, Las Vegas to LA, to Philadelphia to Dublin. The first segment was on American, and the next two on USAirways. The booking had my passport information in, and my BA number for all of the segments.
At check-in at Vegas the agent printed the three passes at the same time, yet only one scored PreCheck.
I suppose it could be that, as the TSA say, PreCheck is random, or there is something odd between the AA and US systems.
As it was, the important (i.e. busy airport) gave me PreCheck, and I was able to connect airside at LA to US, so didn’t need to experience the normal TSA line.
Have you had this problem with US/AA?