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some types of payment must be entered into the CA program as well (592 and 593 withholding are the first ones that come to mind). They have to be entered in the Tax Payments worksheet on the Fed to get them to be picked up on Sch A, but the actual form and all of its details must be entered into the CA program for CA to pick them up.
Some states piggyback on the Fed, Im not familiar with NY or NJ...have you attempted to file them alone without Federal? If they are piggyback states, they wont be able to be Efiled if the Fed cant be Efiled.