I flew into OSL last Tues morn, where my passport was stamped. I flew back to OSL from BGO(Bergen,domestic) then onto Vienna, then to Hamburg and finally from HAM to EWR. After showing my passport at OSL upon arrival the next time a non-airline personal wanted to see my PP was @ HAM before being let into the hold area at the far end of the F gates where my flight among a few others depart from.
At PP control @ HAM they did not stamp my PP for exiting but did check it and swipe it.
So it was if I arrived into JFK went thru CBP and flew all around the US before leaving the US = no PP needs to be shown except when checking in for a flight where Visas etc they dont check or care about, could be a DL would do as well. So the OP ran into trouble for having gone to IST or any place outside of the EU had they arranged a connection in any EU city they would have been fine, sort of like if you have a 1 entry into the US dont fly say LAX-MEX-JFK to get to NY.