My last few polygraphs (I've had well over a dozen of them) were abusive. Before one of the later tests, the investigator tried to establish rapport, and told me that he had interrogated terrorists in the middle east, who had threatened to kill him. Before the test, I sympathized with him on this and thought that those terrorists must have been really bad people. After the test, I completely understood why those subjects had threatened to kill him.
The polygraph is basically a mind fuck. They try to guilt you into admitting some wrong that you've done by pretending that they already know about it. People with a conscience will break down and admit something, but different personality types react differently.
A senior security officer that I knew always passed his polygraphs on the first sitting, and never had any trouble. The reason was because he was a pathological liar. One of the requirements for his job was to come up with "cover stories", which are lies that you must convincingly tell others, to protect the security of a program.
Two co-worker engineers I know failed, because they refused to go back for more abuse. They were not bad or deceptive people -- They were "Type A" personalities, and it was just too stressful for them.
Refusing to take (or re-take) a polygraph is a red flag, and gets a lot of high level attention. The government will assume that you are refusing because you've done something wrong, and may go after you, and could ruin you life, even if you are innocent.