ATC is telling me to go to this runway, but that runway is not the active one. For example, at jfk ATC tell me to go to runway 31R for takeoff, but they are takeoff and landing at 31L

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Sounds like you have overlays installed and you get your clearance from the 'wrong' tower.Just a guess though...Try to get delivery clearance from a different terminal (move your aircraft to another terminal - I suggest the one where the other aircrafts start from - and file a new flight plan).Hope it helpsFrank