I'm concerned about this as well, but the airlines are well aware it would not go over well with the elites

To the OP - the id-checker didn't recognize the bp/elite status/F designation would be my guess. They are trained based on the bp's they see most often and that's what they "know". At Dulles, anything with any sort of status marking would get you in the premium line because all airlines enter security through the single area. Those agents aren't able to be trained to recognize the different bp's, status', etc from all the airlines so it becomes a pretty much anything goes situation.