TRACK DEV. FLC ATC MISCOM IN ROUTING.

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I BELIEVE THE INCIDENT HEREIN DESCRIBED WAS RESOLVED 'INTERNALLY' BY ATC; HOWEVER; IT RAISES A VERY INTERESTING (READ POTENTIALLY DANGEROUS) QUESTION I WILL ASK SHORTLY. MY STUDENT AND I FILED IFR FROM FRG TO N03; BOTH IN NY STATE. OUR IFR CLRNC WAS AS FOLLOWS: FARMINGDALE 2 DEP TO HAAYS INTXN (WE WERE RNAV CAPABLE) VECTORS V374 BINGHAMTON VOR; DIRECT N03. EVERYTHING WENT RATHER SMOOTHLY UNTIL WE WERE TOLD TO GO TO SAX; INTERCEPT V249 AND RESUME OWN NAV. UPON CHKING THE CHART; WE SAW THAT THIS WOULD REQUIRE TWO 90 DEG DOGLEGS; INTERESTING BUT NOT UNCOMMON. WE INTERCEPTED V249 (029 DEG RADIAL) NE OF SPARTA AND PROCEEDED TO V374. 8 MI NE A VERY UPSET ZNY CTLR ASKED US 'WHERE WERE WE GOING? AND NOW THAT YOU ARE IN ZBW AIRSPACE; YOU HAD BETTER CALL THEM!' SHORTLY THEREAFTER; ANOTHER CTLR CAME ON (SUPVR?) AND DEMANDED TO KNOW OUR CLRNC; WHICH WE GAVE HIM. AFTER A MIN OR SO; WE WERE CLRED DIRECT TO BINGHAMTON WITHOUT FURTHER INCIDENT. WHY ALL THE FUSS? THE ZNY CTLR HAD THIS AS OUR RTE: SPARTA; V249 TO SOLBERG; V6 ALLENTOWN; V613 WILKES BARRE; V29 BINGHAMTON; DIRECT. THE QUESTION IS: HOW DID ATC HAVE THIS RTE FOR US WHICH WAS TOTALLY DIFFERENT THAN THE RTE WE WERE CLRED TO FLY? WE DID NOT EVEN FILE A RTE THAT WAS REMOTELY LIKE THIS ONE! OUR ONLY THOUGHT WAS THAT ATC HAD INTENDED TO AMEND OUR RTE; YET A CTLR FORGOT TO ISSUE US THE NEW RTE; HOWEVER; IT WAS SENT TO THE NEXT CTLR (WHO MAY HAVE BEEN OUR ZNY CTLR). WE DON'T KNOW! I MENTIONED EARLIER THAT I BELIEVE THIS PROB HAPPENED WITHIN ATC; AND WAS RESOLVED WITHIN ATC; AS EVIDENCED BY OUR BEING CLRED DIRECT TO DEST WITHOUT ANY FURTHER COM; DISCUSSION OR INCIDENT.