PitchBlack,
You are right to be angry. Polygraph "testing" is a pseudoscientific fraud. The person who told you you've been doubly victimized got it right. All too often, law enforcement officials actually believe their lie detector results, and there is a good chance that you are now the main suspect in the taking of that which was stolen from the video shop.
Regarding the disputed answer to the question, "Did an unknown armed man rob you?" there could be no dispute if it were the practice of your police department to record all interrogations. There is no excuse for not doing this, and your experience helps to highlight the need for such recording.
Your polygrapher's line of questioning about your religious affiliation was completely inappropriate. Moreover, his refusal to review with you the questions he was going to ask
before hooking you up to the polygraph was a blatant violation of standard polygraph procedure, and may have been deliberately intended to help ensure that you would "fail."
For a better understanding of how polygraphy "works" (and doesn't), download
The Lie Behind the Lie Detector and go directly to Chapter 3. You might wish to provide a printout to any who may doubt your word because of the polygrapher's accusation.
You might also consider going public. If you take this lying down, you may unintentionally tend to confirm suspicions that you stole from the shop and made up the armed robbery story as a cover. You can contact your local newspaper, radio, and television newsrooms, and ask to speak with a reporter about your experience, which I think they will find newsworthy. (You can also refer reporters to AntiPolygraph.org; our contact information is
here.)
And name your polygrapher: he (and his bosses) should be held strictly accountable for their conduct. In addition, you can write to your mayor and city council members to complain about the treatment you received. You might also call their offices to seek a face-to-face meeting, which would be more effective. Also, many city councils offer members of the public the opportunity to speak at their meetings. You might wish to take advantage of any such opportunity.