Ok Bean, the way I understand, the JB3 is getting the bit stream confused. If it gets confused, it will record to 44.1k automatically, which sucks, because then your recording will sound either slow or fast (I think slow) and then you have to resample back to 48k, and that really sucks (and if you want to go to CD you have to resample AGAIN to 44k, which really really sux).
One thing I found when practicing with the optical out on my DVD player--make sure that your v3 is outputting a signal first--and THEN hit record on the JB3. If the JB3 is recording with nothing from the v3, I think it's gonna screw you up. Try it out.