The NSA uses what is known as the "relevant/irrlevant" (R/I)technique. You'll find it described in Chapter 3 of The Lie Behind the Lie Detector. You'll find detailed information about countermeasures (including some specific ones for the R/I technique) in Chapter 4.

Based on accounts sent to AntiPolygraph.org, it appears that it is not uncommon for NSA applicants to be subjected to as many as three pre-employment polygraph interrogations. False accusations of deception, such as you've encountered, are apparently not uncommon, and you might get through the process simply by providing your polygrapher with nothing that can be twisted into a damaging admission.

See also the public statements of two recent NSA applicants, Nate B. and "Frustrated" regarding their respective polygraph experiences. (If you'd be interested in making a public statement of your own at some point, contact info@antipolygraph.org.)

You'll also find some discussions of the NSA polygraph program on this message board. Hit the "search" button at the top of the message board. The default search parameter is only for the past 7 days, so you may wish to change this to a higher number.