Breeze,
I still think that audio taping would suffice. And if the applicant passes, and is told right then that they passed, there is no reason to keep the recording. Or, with today's technology, the audio can be burned directly onto a CD on-the-fly in MP3 format by the same laptop the polygrapher is using for the test. I have one CD with 185 songs on it, averaging 6 minutes in length. That's 18.5 hours of audio. Three days worth of polygraphs on one CD. What is impractical about that? And again, I do not advocate giving copies to every examinee. Just make it available to the examinee, or make them pay for a copy if they want one. Plenty of other agencies charge for copies of records, so I'm sure the FBI, CIA, NSA, etc. can do the same.
As for the "other causes", I concede that you have a valid point. (Must not be my day. First Batman, now you.) Biased, incompetent and prejudiced interviewers do cause a lot of people to be eliminated. There will always be people like this, because we're all human. Much like the battle to end racial profiling by patrolmen, it can only be stopped by reviewing the acceptance/rejection patterns of the various interviewers. Not sure about the physical fitness tests. But my health spa is full of electronic weight-lifting machines, stair-step machines, running treadmills, etc. Kind of hard to get the machine to discriminate, don't you think?
Having never actually "failed" a polygraph, I am not a pissed off person looking for revenge. But since I basically "flat-lined" a polygraph that I very evidently lied on, without the use or knowledge of countermeasures, I find the polygraph process to be suspect.