The double lines doesn't have anything to do with either the resizer or the scenery itself. They are probably coming from another scenery, or the AFCAD of another scenery.
First, be sure that you have JFK on top of the Scenery Library, which is were the installer puts it anyway.
Then, if you still double markings, try to use the AFCAD utility to check how many AFCADs your have for KJFK. You should have two and not more: the default from MS, and ours in our folder. If you have more, remove all the extra.