I had similar experience with x-plane, after patching it would error while loading, the guys on the xplane forum instructed me to delete the cache folder, I can't remember exactly but after doing that the game would load with the latest patch. So I'd suggest looking into that. Not sure why you have to do this manually...
I never did get the trackir working either, for something thats fairly straight forward on all my other sims it was frustrating in x-plane.
Don't want to bash it to much,but x-plane 9 is too clunky for me, I'll take a another look when x-plane 10 comes out.
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System - I7 970 : GTX 560 ti SOC : 4gb Corsair ram : Seasonic 620 watt : Samsung bx2450 : extreme 3d pro