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It is obvious that someone who knows how the polygraph works will, in general, produce less accurate results than an ignoramus. Therefore, an informed truthful person is more likely to "fail" than a clueless one. Why doesn't some lawyer somewhere bring this up to save his or her client the ordeal?
The test was designed to be used on ignorant people. If it is being used on someone who knows what's going on, the test is being misapplied and not used as designed. Seems like that might be a due process matter, though my understanding is that different standards for that apply pre- and post-conviction.