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A very informative post. I hear often the mantra that "the polygraph is only a tool, to be used in conjunction with other processes."

I wonder if anyone who has failed a government administered polygraph was actually hired none-the-less due to being exonerated by these other processes.

Your experience is not uncommon. In fact, Congress has officially recognized that the failure rate of CBP, ICE  and SS applicants is over 60%  They stated it was, "worrisome." 
It's also important to know that polygraph are not just imperfect. They are up to the judgement of the examiner. One person interpreting the physiology of another without knowing them. 
In a class action lawsuit against CBP,  it was stated that 14 applicants were told the reasoning behind one particular series of questions. You may remember them. The examiner asked if they mediatated, we're on medication, could often remove themselves from a stressful situation, etc. They were told that it was important to know because if they were able to mediatated or otherwise control theory physiology, the results would be difficult to discern. If simple breathing techniques and meditation can throw off their system, how accurate can the system be as a whole?
Furthermore, applicants are told, in a written portion of their application, that the polygraph is not a catch all, and that it will be used in conjunction with a thorough background check to see who gets a job and who does not. Every failed applicant can tell you that is simply not the case. The polygraph is the end of the road, no matter your record, grade, education or references. 
The test is keeping great applicants out of the system, and is a blatant waste of resources. At the very least, the polygraph should be one of the first steps in the process. Some applicants spent over a year of time and effort to get to that point, losing time money and resources only to be removed from selection by one exam. 
My advice, contact your congressman. Get involved in removing the polygraph from new hires, or at least amending the questions. Good luck. You're not alone.

Took it in August of 2014. Female administer. Lasted 6 to 7 hours. Last 3 questions were repeat because she wanted to make sure. 
  The question? Have you been involved or are involved in any illegal activity be it selling narcotics, illegal items such as firearms, stolen property , etc. while at work during business hours or off?  All 3 times I answered no. She insisted I was lying. For the last 3 hours she berated me into telling "the truth" and admitting that I was doing such a thing,  Oh and that I have associations with the cartel, imagine that. I later told her "with all due respect maam but, when you asked me the question I was not even thinking about the question and answered no". She kept saying that the instrument is accurate and that it shows I am withholding something but that when that question was asked the "graph markers or meters lit up and were all over the place". I stood my ground for the next 3 hours and said "I have no idea what you want to hear or what to tell you. I have never done any of that in my whole life, nor will I ever, or ever think of doing that. Especially since I work at a school. WHy would I put these kids, my own well being, and the well being of my family at risk by doing such an irresponsible activity?" Then she says "well you tell me" 

     Another test again, by this time I have a splitting head ache, my eyes ache, I have gas, my ass hurts, and I am drowsy. Every so often my eyes would water or become dry. She becomes impatient and tells me to quit moving, to quit moving my eyes, to not breath so deeply. I explain that I am trying not to fall asleep. Then she sits back and says " I am insulted" . I apologize and said that I am just too relaxed is all. Then she says "well don't relax, don't meditate. Just let nature take its course". In my mind I am thinking this is BS, lets just get this over with now. In fact I was close to getting up and walking out, it was so ridiculous. She kept repeating to not meditate or relax too much. I mean, come on, really? 

   Between sessions she lectures me on telling the truth and explaining about life and about how truth and honesty affects our lives in ways that has nothing to do with this machine. Each lecture takes 30 to 40 minutes each. Then hooks me up again to the machine. Explains later that she would hate to see me lose this opportunity to land a job in this field. She says I have the right demeanor and physically fit for being 40, and believes I am right for the job. I explain that I didn't get an opportunity to join the military and this is the one way I feel I will be able to serve my country and community. 

So, it continues and the last 15 mins or so she is impatient with me because my eyes are moving, my nose starts to run, and my head and neck is hurting. She keeps asking me why I am lying. I tell her over and over again I am not. NOW, I think my mistake is this....so all of you reading take note. I think my mistake is that I told her that "I have no idea why it is "supposedly saying" that I am lying, I told her I remember back in high school carting friends around who were hoodlums, or thuggish, but because at the time I had shady friends, a couple of times my friend would ask me to take him to another friends house to pick "something up". Well at the time how am I supposed to know. I don't think anything of it. But this was 25 years ago. I have never spoken to these people since. Nor associate with that kind anymore. I was a skater then but had the occasional black sheep in the bunch who most likely sold drugs to my other friends at the time." But then she interjects saying "that's years ago, we're talking about now"  But then says later as I was explaining, "how did you not know they were dealing? you had to have known". I told her I didn't, I may have had a feeling but I didn't pay it no mind cause I didn't care at the time. I wanted to be the cool friend. So after that she said "ok, well, I will put this in the folder and give it to "Quality Control" and they will take it from there. Sounded suspiciously like " hah, I got you". but who knows, I was glad for it to be over. Its all bullshit. 

I am not sure if they flipped a coin and it landed on the side that said "fail this chum" or because I was trying to find a rational reason why this contraption was actually reading a false reading. In a way, I think I was trying to appease her, but at the same time explaining that it was a long time ago but that it was just an idea. I think what these goons are looking for is someone who has "no conscience", no guilt, in the event as an officer, you are involved in something that isn't quite your fault, so to fudge things, just leave a few half truths out, out of mind totally, and "stick to your story".