JA's tend to not hold sorting very well either, just in general (as soon as you change jobs most JA's go back to wherever the hell they want, this is annoying since some jobs, like DNC, rely heavily on a massive selection of JAs).
I think they really need to do some "tweaking" to this function of the game so things can "stay" sorted properly.
I never did the xbox-to-pc back and forth thing when playing, but you might want to try 'forcefully' backing up your settings at the character select screen before you get on your xbox (I forget what it is, something like shift+cntrl+b at character select). I don't know if it takes into account magic sorting, but if it does you could just reload the settings file before your next PC session.
Posting from just above the generator.