Serious audio trouble. 44/48 sync problem

I am posting this here too because maybe music and audio savvy people are over here as opposed to in the OSX forum.
I'm not sure if I need to contact Apogee support or call Apple. I use an Apogee One audio interface.
Despite how I have my apps, OSX Audio Midi Setup, and my Apogee One set (everything set to either 44 or everything set to 48), I always end up with an audio sync problem with Photobooth now in Mountain Lion. It never occured before I upgraded. It's far too out of sync to simply be a system resource issue. It's cleary a 44/48 descrepencey. It's way out of sync. If I go into Audio Midi Setup and ensure everything is 48, restart my computer, then Photobooth works fine. Yet the second I start up an app like Garageband, the Photobooth audio jumps way out of sync. Despite having the Garageband settings right (In GB audio settings I've tried both "System Setting" and "One") This happens regardless of what app I use - GB, Logic or Kontakt - all set to whatever the system settings are.
This is beyond frustrating as I need to make videos for school while I have my audio apps running.

UPDATE: The problem occurs even when the Apogee One is completely disconnected. While I am troubleshooting I am now only using the iMac onboard audio and mic.
I understand now that Garageband only works in 44100, so it's possible that if I had other things set to 48000, that starting Garageband would force some changes that might mess things up a bit.
So I'm only working with Kontakt now which I am absolutely certain is set to 48000. I ensure that all the settings in OS X Audio Midi Setup are set to 48000. Restart the computer. Photobooth works fine, until I start Kontakt. Once I open the app, even before I load any samples, Photobooth audio sync delay occurs and it's REALLY bad. I check the OS X Audio Midi Setup settings - all are still set to 48000. I verify that Kontakt is set to 48000, and it is. So I'm at a loss. Apple might be losing me over this.

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--------------------------------------------------------------------------------
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