Logic Pro has a couple different ways it finds the device being used, and has some settings that seemed persistent, i.e., that it'd always try to use that device.
It's been several months since I looked at it... I'm having too much fun with the Cygnus beta... but I'm wondering if Logic isn't doing something that causes the FM3 or AF3 to lose its connection and/or act up. I've been considering building an external boot disk with only Logic Pro on it and see if that'd recreate the problem I had.
I started thinking along this path because I had all sorts of problems with my FM3 dropping connectivity with FM3-Edit. I had Logic Pro installed and configured to use the FM3, then was seeing something I didn't like on my Mac (because it'd been initialized from a backup from my old MacBook Pro), so I wiped the disk and reinstalled the OS, and have not reinitialized Logic Pro, and, as a side effect, haven't had FM3 lose its connection or freeze. (Well, I had it freeze, but that preset was overloading the CPU.)
@BryantP have you seen anything like that or do you have a Mac with Logic Pro on it in the lab? I had a series of email with Matt as I tried debugging the dropping situation; Initially I thought finding a "happy" USB port fixed it but I question that now as I've moved to other ports that'd previously had problems and they're still good and Logic was pretty invasive that way.
I'm not a Logic expert, but maybe if we had someone who knows all the connection preferences and the USB behaviors maybe they'd have insight into the problem.