There must be another scenery in conflict. You can verify yourself the ILS at JFK are correct, by opening the AFCAD file with an FSX AFCAD utility, like ADE. There, you can see the ILS is having the same heading as the runway (note that both will be listed as true headings, not mag.)
NOTE: the 22R, instead, IS an offset-ILS, so it's supposed to be not aligned, but this is just as it is in real life.