If it was a video settings problem, I had this everywhere, not only in JFK
That's just an assumption that has no real technical base. If this is a bug that happens only after a certain amount of video memory has been consumed, and after a certain combination of shaders and materials has been called, it's very likely you wouldn't see anywhere else, if the conditions are not met, without this being a problem with JFK in itself.
And yes, I've seen it at other FSDT sceneries too, but couldn't find a cause that could be related in any way to how the sceneries are made, it's just that not many sceneries out there have custom jetways, so there's not much to compare against, perhaps FSX has a bug with custom jetways only after a certain size, either in the jetway itself, or in the overall memory usage of the scenery, and this can change by area.
I'm saying this in order to save you from wasting your time with uninstalling/reinstalling JFK or finding duplicates. If the problem is exactly as you described ( perfect jetways overall, which splits in two ONLY when they move ), it's not a problem of the scenery and it's not a problem of a duplicate scenery. Just accept the fact that the FSX jetways are bugged, just like the sinking wheels problem, which randomly affect jetways everywhere.