The red X indicates missing Simobjects, most likely jetways. Since you already said you removed the .INI file and updated JFK, the problem is clearly nothing that has anything to do with JFK or GSX.
Instead, other users reported Red X at JFK, because they tried installing DD, and then wanted to go back to FSDT JFK, and failed to properly uninstall the DD scenery, so those Red X are caused by remnants of the DD scenery still there. Likely their SODE jetways XML file.
