I'm not giving you this comment as having tried it first hand, because I haven't tried OrbX products BUT, one of our testers wrote on his blog that it wasn't too happy of FTX because, even if it was really nice if you were flying in Australia, it was just too invasive for his tastes, because it made some havoc outside Australia, with big geographical features missing, because the product makes many changes to default scenery config files, that have an impact even outside their covered area.
As I've said, I don't know about the details, I would point it out to that blog, but unless you could read italian, it wouldn't be too useful. Perhaps, he'll would like to contribute it here.
Perhaps, when you disable FTX, it might not properly restore your scenery.cfg as it was before, that's just a guess, but it's consistent with what you are describing, that you need to reinstall our sceneries to use it again. You might probably fixed it by just re-adding them to the Scenery Library. If this is the case, then it's surely a problem related to the scenery.cfg not being properly restored.
Just check, after disabling FTX, if JFK, Zurich and Geneva are still there, and if they are, if they are still at the topmost levels.
