furger / Virtuali,
I noticed this issue before when I was reinstalling KORD and KJFK. I found that Windows (Vista 64 in my case) did NOT uninstall the previous version information from the Install Programs in the control panel and both version were listed, causing some strange disappearing/missing building and terminals at both these facilities. So, I uninstalled all versions of those airports in Windows' Install Programs in the control panel, rebooted and re-installed the newer versions. Then, Launched FSX, checked the Scenery library for the folders, clicked the OK button, and then shutdown FSX. I finally rebooted and then re-launched FSX and all was fine.
I mention this here because it work for me each time I installed the updated sceneries and it might do the same for you.
Good Luck!