@FinalSaga
I have set the song setup window to be at 48khz, but I still get the following pop up message (screenshot below).
Also when I look back in my Apogee Maestro settings, it's magically switched itself back to 44.1khz.
Though the song page remains on 48khz, this still is an error as the Apogee is showing 44.1 and for all intents and purposes it looks like Studio One 3 is dealing with the session in 44.1khz.