Also, the sc48, computer, and AES output to my studio monitors are the only things in the system right now, I would assume the Avid is running on its own clock and should be outputting it to the computer via FW?
One new clue I found is that on an empty project it either stops counting at 12000 samples, or at 12222, depending on how long the MIDI "prepare using:" buffer is. Oddly to me, the higher buffer makes it stop at the smaller 12000 number. I'm not using MIDI, I forgot what tab I was on when I was adjusting it.
Also, Windows audio outputting to the SC48 is set to 32 bit, and has always worked fine (though there is no timecode to follow for Windows). The documentation (and Cakewalk) say the settings should be locked to 24bit. But whenever I start trying to change the windows setting to 24 bit, Cakewalk starts bluescreening a WDF violation on loading a project. Sample rate is 48k across the board.