These are all questions that came to mind after I took a polygraph. Being naturally inquisitive, it only felt fair to ask some questions during the polygraph but I was interrupted each time. 
If you'd like to answer any based on your experience I'd greatly appreciate your input. Thanks!

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Has a former polygraph examiner failed the polygraph despite telling the truth? Did that change their attitude?

What are some of the reactions of polygraph examiners to false positives supported by new evidence?

What are some of the reactions of polygraph examiners to false negatives that are later proven with evidence?

Do polygraph examiners use black and white thinking?

Do polygraph examiners have any concern for undiagnosed health problems?

Are polygraph examiners aware of different level of human sensitivity?

Do they care about the ambiguity of results that could simply be one reacting to someone he or she does not know? 
(If we are going by the machine itself then couldn't a loved one ask the same questions? If its solely the polygraph machine at work here then there should be no problems.)

Do polygraph examiners have a general personality type?

Is he or she aware of logically flawed arguments in their favor?

Is the hurt done to innocent people not important because some people confess to polygraphs?

Would less people confess in an interrogation without a polygraph?

Do people become polygraph examiners to find out the truth or just to act as a prosecution?
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My questions are all about how the polygraph examiner affects behavior and if he or she is actually aware of it.

Steven, 

I'll take a chance and answer truthfully for myself only.  Other examiners may have differing opinions.   

Has a former polygraph examiner failed the polygraph despite telling the truth? Did that change their attitude?

Yes, I am a polygraph examiner and I failed one polygraph, requested a retest with another examiner and passed.  I know there are false positives and the first examiner was not very professional.  I did not use countermeasures on either.  My attitude is the same, there are good and bad examiners, like good and bad teachers, choose carefully.  My attitude remained the same, polygraph is not 100% accurate and should be used cautiously.   

What are some of the reactions of polygraph examiners to false positives supported by new evidence?

I am not sure what “New Evidence” you are talking about.  I have been aware of false positives my entire career, and I give every individual an opportunity to explain why reactions occur, I will retest if necessary to find the truth.  Never use polygraph as the determining factor in any case or situation.   

What are some of the reactions of polygraph examiners to false negatives that are later proven with evidence?

I am aware of false negatives and do not support using polygraph as the only investigative tool.  Use all of the resources available to you, polygraph being only one of many.   

Do polygraph examiners use black and white thinking?

Not sure what you really mean.  You are truthful may be White, you are not truthful may be Black, and I don’t know (Inconclusive) is Grey?  If that is your meaning, then Yes.
Do polygraph examiners have any concern for undiagnosed health problems?

Yes

Are polygraph examiners aware of different level of human sensitivity?

Yes

Do they care about the ambiguity of results that could simply be one reacting to someone he or she does not know? 
(If we are going by the machine itself then couldn't a loved one ask the same questions? If its solely the polygraph machine at work here then there should be no problems.)

No, we establish rapport in the Pre-test and proceed to testing after rapport is built.  Otherwise I will not test.   

Do polygraph examiners have a general personality type?

No

Is he or she aware of logically flawed arguments in their favor?

You need to explain what you mean on this one.

Is the hurt done to innocent people not important because some people confess to polygraphs?

No, I am concerned about innocent people, and it is important that I not get a false confession.  It is important that I find the truth.   

Would less people confess in an interrogation without a polygraph?

Depends on the interrogator.   

Do people become polygraph examiners to find out the truth or just to act as a prosecution?

Personally, to find the truth.  It does not always happen and polygraph is not 100%.  Not all examiners share my beliefs and convictions.   
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My questions are all about how the polygraph examiner affects behavior and if he or she is actually aware of it.

Hope this helped

If I have an opinion prior to conducting a polygraph, (I think your guilty), I don't conduct the examination, I would be biased and my attitude would skew the result of the examination.  I can listen to both sides and conduct a "Fair" examination.  There have been cases in which the investigator has a strong opinion regarding the test subjects guilt, that is his opinion not mine.  If his opinion has been communicated to the test subject it takes time to explain I don't share the investigators opinion, I am interested in the truth only.  In some of these cases, the examinee has produced polygraph results that indicated their honesty to the questions being asked.   

My personal mannerisms are not shared by all examiners, and I could be very wrong in my attitude and opinions, I listen and learn daily about polygraph and truth.  I have had false positives and false negatives in my career.  I hope I have learned from these experiences and use caution in conducting all examinations.  Polygraph is not 100%, it is a good "Tool" and a tool only.

"Polygraph is not 100%, it is a good "Tool" and a tool only. "

However it would appear by a high number of respondents in these forums that many fail to be hired, to be allowed to make a living, support their families and themselves "because" of this "tool." While you (individually) are not responsible for how your tools data is reviewed and used you are still a part of that process and could be, at least potentially, just as responsible because your tool hurt someone. 

I doubt anyone can 'know' the complete truth about another person. Certainly in hiring issues where security and integrity are prerequisites the deep dive surrounding background, character and traits would be understandable. But take the candidate that passes all those, the tests and the background 'and' the psych (as many on this forum attest to) and that "tool" shoots down their chances at employment?  Individual traits of examiners aside, that is an indictment and the Polygraph is guilty as are the locations, businesses and organizations that (often) it would seem rely on them for that yes or no decision. 

Tools are interesting. There are scalpels, the tool of the surgeon and their are clubs... I'm leaning towards the poly belonging to the later. A rough tool to be associated with...