Unless the examinee signs an agreement stipulating otherwise, polygraph results are not admissible as evidence of guilt in any criminal court in the United States. You won't be prosecuted simply for having a false positive outcome.

However, anything you say to your polygrapher may be used as evidence and might potentially launch a criminal investigation. There is a case, for example, where an NSA polygrapher twisted a statement by an examinee into an admission of downloading child pornography and then made a criminal referral to state police.

As for signing over rights, yes, it is common for agencies to require applicants to sign a waiver form agreeing not to sue them. This should tell you something about the ethics of the polygraph "profession." As an example, see the form used by the Los Angeles Police Department:

http://antipolygraph.org/documents/lapd-polygraph-waiver.shtml

retcopper,

The answer to the first part of your first question found in the penultimate paragraph of the above-linked statement. While I don't know what the ultimate outcome of this person's case was, a Defense Office of Hearings and Appeals administrative judge ruled in favor of the applicant in a similar case:

http://www.defenselink.mil/dodgc/doha/industrial/02-12199.h1.html

I recently took a poly for a Federal government job.  I signed a statement that preserved the agency's right to pass any incriminating confession along to the appropriate authorities.  I presume that if one were to confess to some major crime, they could be prosecuted.