I failed a Agency poly in 2003 and have just heard that my appeal was denied (no surprise).  For the last few years I've had a IR on my clearance in JPAS waiting for final adjudication from the Agency.  Back in Feb 2010 my Final DoD S went inactive as the contract I was working on ended.  I'm on a new contract now and my S will need to be re-activated.  DSS is requiring me to fill out another SF86 of to which I fully plan on answering that I've been denied a Agency clearance.  When DSS see's this will they automatically deny my S, even if I have had one before that wasn't terminated for adverse information?  Since it's a S would they just run credit and police records like the first time?

I'm not the original poster but I wanted to give everyone an update as I'm in the exact same situation.  I was denied clearance (yes, clearance denial, not suitabiltiy denail) by the CIA because I failed their pre-employment polygraph exams a couple years ago.  I had a DOD clearance that went inactive when I left that company.  I appealed my CIA clearance/sci-access denial.  I too have the Incident Report in the DOD JPAS security clearance system due to the failed CIA poly and I don't think the DOD will adjudicate me for another clearance until my CIA appeal comes through.  So if the OP waited 7 years, I guess I'll be waiting 7 years too (though I was told by the CIA that appeals take up to 2 years).   

I had to fill out another SF86 for the DOD (new job) Secret clearance and I've been waiting almost a year so far for my clearance because of that Incident Report still being there.  If my job had known I would have trouble getting this clearance, they wouldn't have hired me, and they will probably dismiss me at my 1yr mark as some form said they could do if I'm not cleared by then.  No other contractor will bother hiring someone with an Incident Report in JPAS, so we can kiss our cleared careers goodbye (for about 7 years apparently).  Luckly, I have another job lined up and will be dropping off my resignation letter to my boss in a few weeks.

It seems like me, or anyone else, won't be flat out denied a DOD clearance or any other clearance because of the stupid CIA's polys, but you can expect to have your other clearances in limbo for years while you wait for your appeals (if you appealed) to come through.  In fact, you may be better off not appealing to the CIA if you don't feel like waiting, but then you'd be admitting guilt and letting those rat bastard polygraphers win.  Either way, it is a losing situation for myself and anyone else who is dumb enough to take a polygraph.