you can record to the mt at 24/48 _and_ to the jb3 at 16/48 simultaneously.
now i have the oade w+mod, and use and iriver, but i dont believe there would be a difference in your setup. now that i reread your post, can the jb3 record at 16/48?? i have never owned one, but if it does, you are golden.
why record at 48 instead of the full rate of 96?? well, this way, your recording will work like the above, and you can run your cf card in the mt for a full 2 hours before the track split. at 24/96, you will only get 1 hour record time. and while the optical out is able to truncate the last 8 bits, it cannot resample sample rates.