This DoD agency is undoubtedly the NSA (big secret).
As a former NSA employee, and now a contractor to
another Intel agency, I know that the DSS does not
look at the poly results, but only what you were 
tricked into admitting.  The NSA relies heavily on
peoples' ingnorance and fear, because they now ask
applicants, if they have done any research on polys on
the Internet.  My polygrapher, "friend",  asked if I had
ever posted to this site and what usernames I had
used; I told him, because I just didn't care.  Truth be
said, the NSA used to tell employees  not to discuss the
poly questions with co-workers.  Unless you admitted
to something significant, don't worry about losing your
Secret clearance, although, the failed polys may make
it more difficult to upgrade your clearance to TS.   
Unfortunately, your security officers won't tell you
about this dilemma.  I do know, that the Intel agencies
share a common database, that reflects SCI clearance
accesses, or denials.  The CI, counter-intelligence,
poly is easier to get through, than the full-scope poly.
When I see, full-scope polys, advertised on the
Internet, for software developers, I just have to
laugh, because I know what a "crock" the polys are.
All those poor bastards, working for the NSA/CIA, that
still don't know the truth, and live in fear of 
"big brother" !

Of course it is !  The examiners use lies and trickery all
the time; they don't give a damn.  My NSA polygrapher
pretended not to know about the use of
counter-measures.  The whole procedure is very
scripted and amaturish.   Does FANX ring a bell ?  Isn't
it interesting, how all those disfunctional people still
feel the need to be controlled, in such a disfunctional
environment ?