Garage Band 09 Changes Core Audio

I upgraded to Garage Band 09 on my aluminum 20", 2.4G Core 2 Duo, 2-GB RAM iMac. I record through a Lexicon Omega USB interface.
The Lexicon Omega has three possible USB interfaces: Channels 1-2 I/O; Channels 3-4 I only; and Mac USB. One chooses the interface using Audio MIDI Setup.app. I chose the first option above, which was the default offered by the app to set the Mac's core audio system.
I then launched the new Garage Band and, using GB's metronome for tempo, laid down four guitar tracks. Very nice and easy!
I then wanted to include a software drum loop. As soon as I chose it, GB said it had to download 1.1 GB of updates. OK...I did so. Relaunching GB, I now had my loops, but the audio input, under "Preferences", was now Mac USB. No external others were available. The guitar input now had insufferable latency.
Please don't offer to tell me to do all of the anti-latency things. Bottom line is it worked, and now it doesn't.
I can quit GB, launch Audi MIDI Setup, and set it again to Channels 1-2 USB. But as soon as I launch GB, it changes it to Mac USB with no other choices.
Why is a program such as GB allowed to change a core system setting? How do I fix it? It has ruined my ability to use the program.

I have the same equipment you do, and have been encountering similar problems. Sometimes I've had Channels 1-2 available, sometimes Mac USB, and sometimes, as right now, Audio Midi Setup cannot connect to the Lexicon Omega at all, although its icon still shows.
USB is finicky, and with a dozen USB devices it can be a trouble-shooting nightmare. I'm going to look for a firmware update for the Omega. I have a Logitech Harmony Universal Remote (USB, IR, with an RF Extender) which was nearly unusable for two years until a recent firmware update corrected the connection problems.
Please, let me know if you learn anything!

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