Back from the land of dead threads! I just realized I never reported back. It ended up being of my own doing, like most of my problems in life!
On the 09 990Advs there are two black keys and one orange key, except the orange key isn't a key. The dealer I purchased the bike from didn't send my the owner's manual so I didn't get the orange key thing sorted out until I got through to somebody at KTM-NA and they emailed me a copy of the owner's manual which emphatically stated that the orange key isn't a key, but a code tool to deprogram and reprogram the actual keys. When I grabbed the code tool and used it as a key it disabled the ignition and the other keys until I used the code tool once more to reprogram the keys.
Once I got that sorted the creek flooded and washed out both crossings so I had to leave the bike out there for most of a week. I finally got a friend to go out there in his lifted superduty since the county didn't want to repair the crossings until the water had gone down, and it was still high enough that I was wary of ending up in a similar situation if I attempted to ride across.
Other than a problem with crud in the tank fresh from the factory and a clogged fuel filter that the dealer took three tries to diagnose correctly, the bike has run like a champ!
I took it on a trip to big bend a few months ago and it performed flawlessly.