Once you get through the polys, NSA will direct the
DSS/DoD to start the TS background investigation.
For the TS, it is taking at least a year, once that is
completed, then your case still has to go through NSA
adjudication.  Adjudication can also take up to a year,
or more.  Also, NSA is getting very anal, so don't hold
your breath, about getting in.  I waited two years, then
went with a different Intel agency.  Good luck !

You have the NSA clearance process in the wrong order;
first is the poly, then the TS background investigation,
then NSA takes the two results through the adjudication
process.  In my case, I was an ex-NSA employee with
some issues that were cleared up over two years ago,
but NSA did not have enough to reject me (I am sure
that I could have won, through appeals), so they will
just sit on it, until you give up.  So in my case, I said
screw it, and went with a different agency.  What is
important, is gettng an SCI, with DIA, NRO, CIA, etc.;
it always looks good on a resume.

It isn't necessarily true that the polygraph comes first, and two years is an outside case for the length of time for the screening.  I don't know much about the process for contractors, but for regular employees, it usually takes 4-5 months and the background investigation is started as soon as security has the SF-86 (which is sometimes before the poly and sometimes after, depending on the path the employee follows).  I'm afraid I don't know whether it's true that third polys are taking so long.

Have you tried to talk to whoever is in charge of your recruitment about this?  The HR people generally don't know a lot about what's happening in security, but s/he can probably tell you if something has been decided on the poly and may be able to push for a quicker third poly.

Good luck!

I think Mr. Guest is wrong about the length of time to
get cleared through NSA and DoD/DSS.  I read that OPM
is backlogged around 150,000 clearance cases.  I had
been an NSA employee, for many years, and know what
I am talking about.  The time frame, between failed
polys is about three months; add to that, the
investigation time for the TS, and the TS adjudication,
then the NSA adjudication, it can take up to two years.
If you don't have any significant issues, or foreign travel,
then it will probably take less time.  I empathize with
you about trying to find a good job, without the
TS/SCI.  With only a TS, at that time, I didn't find
anything good, until I got cleared for TS/SI with a
different agency.  How do you want to communicate ?
By the way, there are a lot of disfunctional people at
the Agency, and I am enjoying working with my 
customer much better.

Oh, and I forgot to mention that the OPM being so backlogged has nothing to do with NSA.  DSS does NSA security clearances, and OPM uses a different agency.