Same thing happened with me at the CIA last year.  Only I didn't get a "thin letter" in my mailbox.  No no no, the CIA was nice enough to send me Certified Mail, where I had to sign my name so they could be sure that I received my rejection.  The lovely packages were delivered to my door two months after the famous 3-day (which includes polygraphs).  I had been disapproved for access to classified information because some junk machine didn't like how my body was reacting.  I got the reason for my denial, some information with a bunch of stuff censored out regarding the evaluation of my polygraphs, how to appeal, and other stuff.  I'm thinking of posting the whole boondoggle publicly online and putting the CIA on blast, just like this guy did.

I understand your plight, having had a similar experience myself. I'm sorry to say that this could indeed screw you for future federal jobs, but it's difficult to know for certain. If there are other job opportunities that interest you, I think it would be worthwhile to apply for them.

I took a pre-employment poly with FBI about a month ago and got the "thin" letter.  Ever since I have been obsessed with playing the details over and over in my head.  My poly was performed just as told in the Truth Behind the Lie (examiner telling me he is here to help, etc.)  I have had trouble sleeping and am upset thinking this could screw me for future federal jobs.  Any words of encouragement?