Whenever you have missing jetways, the ONLY think the can cause this, is a conflicting .BGL from another scenery, or a traffic product. There are no ways to remove jetways, other than from another .BGL so, whatever is causing this, it's a conflict caused by another file.
And yes, of course FSDT KORD comes with automatic exclude areas, but some items, like effects AND jetways, are bugged in the sim (a bug which has been there since FS9) and exclusions don't always work correctly, so the only fix is to find and remove the offending files.