Flight Crew Multiengine; Flight Crew Instrument; Flight Crew Air Transport Pilot (ATP)
Situational Awareness; Communication Breakdown
ATC Issue All Types; Deviation / Discrepancy - Procedural Published Material / Policy
Air Traffic Control Issued New Clearance; Flight Crew Became Reoriented
Human Factors; Procedure
I loaded the route into the FMC. We received and acknowledged revision 1 sent from Dispatch asking if we had received the revised flight plan. It was the route I had loaded earlier. It started with the ZZZZZ departure. But the route assigned in FD Pro did not match the route from Dispatch; but it too started with the ZZZZZ. I assumed the FD Pro flight plan was the original flight plan. We received the PDC clearance which stated 'Cleared to the ZZZ airport ZZZZZ then as filed; climb via SID. Expect FL340....' After takeoff; prior to completing the ZZZZZ SID; BOS ATC requested we fly direct to ZZZZ intersection as a short cut. We searched our legs page in the FMC but could not find it. We advised ATC we had no such fix. They had us go to ZZZZ regardless.  They then asked to confirm the route we were flying. The route we had loaded from Dispatch was NOT the route ATC had on file. But it was the route that was originally in FD Pro for [us].  ATC then had us fly that earliest FD Pro flight plan to ZZZ. We were asked later during our flight to call BOS Center once on the ground. I did. They wanted to figure out what might have been the reason our flight plans did not match up. They said we had not deviated off course as we were on the filed ZZZZZ which was on both flight plans. I stated to him I had loaded the revised flight plan from our Dispatcher and that I accepted the PDC flight plan clearance message as it appeared to match our revised flight plan.  I called our assigned Dispatcher and informed him of the problem. He thinks PDC did not load the revision but he should have gotten some kind of rejection notification if it was kicked back. Which he did not. So we do not know why ATC did not get the revised route that we flew. I would suggest that if the ATC PDC message that acknowledges our clearance was a complete route; not 'as filed'; I would have caught the discrepancy in the flight plans. It was unique in that both flight plans began with the ZZZZZ. It worked out in our favor that ATC gave us a short cut before we left the ZZZZZ. If not; somewhere after the ZZZZZ we would have deviated off the ATC filed route. The route that Dispatch sent us matched the route in [our] flight plan. The PDC acceptance message was not enough to make us doubt we had a route difference. PDC clearance could read the full route instead of 'as filed'.
Air Carrier Pilot Flying reported a confusing Pre Departure Clearance.