I took my first poly last week as a condition for employment.  I wish I had known about this site or had at least researched the polygraph.  I figured I was going to be honest and had nothing to fear, I did have some concerns I over analyze things too much.   
I met with the poly operator, very nice polite, he asked the questions and I answered honestly and in great depth.  even after I had answered a question a memory came forward and I presented it to the poly operator.  There have been some things that I have done in my distant past that I am very embarrassed about, thing in my early twenties.  Some of them minor infractions of the law others just go against my current morals and beliefs.  I talked to the poly operator for over three hours before getting hooked up to the machine.  I made a joke about the chair being "old Sparky".  I wish I could remember the questions better but, I can't.  One question was; is my name ***?  Do intend to answer all the question truthfully?  Have you ever committed any illegal sex act?  Have you ever used excessive force?  Other than what you have told me have you ever used any illegal drugs?   
The poly operator ran me through the ten questions 3 times.  After the set of questions he asked me if there were any questions I thought I had a problem with and being to honest I answered.  The pre-test interview lasted so long I had a dry mouth.  I was told to breath normally and not to swallow.  The first set of questions I think I had to swallow after each question.  The next set of questions I was reminded not to swallow, I tried not to swallow but I had to several times and one time I caught myself.  Before the third set of questions I asked for a drink of water, this only help a little I still had to swallow a few times.  Me not swallowing  caused me distress.  After the 10 questions three times, he gathered up all the charts and left the room.  He came back in and said he was going to ask some more questions.  This pretty much told me the results were not favorable to me.  He asked me the 10 questions two times each.  He unhooked me and left the room.  When he came back in he told me there were signs of deception, about the sex question, the drug question and the use of excessive force question and then he said there were deception in some of the police questions.  I have worked in law enforcement for 8 years, the times when I have had to use force to make an arrest are very limited and every time was justifiable.  The drug use I told what I had used and when was the last time I had used over 15 years ago.  The sex question other than having sex with a married woman while I was in the Army I had never done any of the examples the poly operator listed.  I left the room feeling utterly despondent/depressed, I was in disbelief.   

I got home there was an e-mail telling me the job offer had been pulled.  I still have questions about my recourse.  Any advice?  would swallowing during the test make any difference, will my embarrassment about the sex question make a difference, why did he come back into the room and ask me more questions when he had told me he was only going to ask the same 10 questions 3 time each.  When he told me I was being deceptive he said he had consulted another poly operator and they had agreed to the results, was this a ploy, the chance of 2 poly operators taking 5 hours to interview me i find far fetched.  Any suggestions welcomed!!

I can't think of a single good reason why a person shouldn't be allowed a few sips of water between question series. I believe an examinee should expect the cardio cuff be deflated, given an opportunity to adjust their position if needed and take a drink if they need one between each question series. On the other hand when someone can't seem to remain relatively still for a 3 to 5 minute question series, or makes the same movement at the same place on every question, whether before or after, once being cautioned they begin to appear non-cooperative. 

If the data has been trashed by movements, the opinion of the examiner should be that no conclusion was possible based on unscorable data. The subject should not be called deceptive based on unscorable data. The examiner is also entitled to articulate the circumstances and render his opinion as to whether or not the person taking the test was deliberately trying to alter the data.

If someone is stressed to the point of severe dry mouth, berating them about swallowing isn't likely to make things any better.  A water break or even taking enough time to allow someone to dissolve a cough drop is generally more productive.

As to why 2 additional question series were collected, based on your description of the test, I believe that the format being used recommends 2 additional question series if after the first 3 question series are collected,there is still insufficient data to render an opinion.

If after the 2 additional question series there appears to be enough data to render an opinion of No Significant Reaction, then testing is concluded. If there is enough data to conclude that their were significant reactions to relevant questions then current American Polygraph Association Protocol calls for additional question series focused specifically on the reactive areas and does not allow a finding of deception unless the new tests are conclusive. If the last 2 question series had the same problems as the first 3 then the proper finding would be inconclusive.

However, your examiner may not follow the APA protocol. If you are in a state that requires examiners be licensed then a formal complaint will trigger a review of the examination by someone not connected with the agency to which you applied, such a review might disclose the information you seek. 

Polygraph examinations routinely take a 2-3 hours if everything goes well. 

Even though some agencies require an excessive force question for experienced officers, I don't like it because every officer who has ever had to use force, whether justified or not has been second guessed by their co-workers, administrations, the public, and even themselves. If it was justified, it isn't relevant to their suitability for employment and if it wasn't, it should show up in their background investigation. I prefer asking if they have failed to disclose any previous disciplinary actions. It accomplishes the same thing without putting a good cop on the defensive.

Any agency that would blackball someone because he had problems with another agencies pre employment polygraph, probably wouldn't be worth your trouble any way. I have heard of one guy who failed 3 polygraph exams before he found his career agency. Keep trying. 

I also had a breathing issue and I thought I was breathing normal until the examiner told me otherwise. Everything was inconclusive. Then about the third time- I had put my head back and the saliva build up in my mouth caused me to swallow a lot and that test also was scratch. How accurate can this thing be if swallowing messes it up?