OK, so this means
1) you have tested iPod 1/8" out > JB3 1/8" in with no problems - both channels work.
2) Tested with (2) 1/4"TRS > 1/8TRS > JB3 1/8" in with only Left channel
3) Reversed (2) 1/4" TRS > 1/8"TRS > JB3 1/8" in with only Left channel.
Is this correct???
If so, I believe the cable is not seating correctly in the 1/8" input on the JB3 and you are sending both signals into Left and nothing into Right.
Terry
if you are using the same exact cable for the ipod > JB3 as you are using for the (2) 1/4 > JB3 then it has to be the 1/4>1/8 adaptor
if you reversed it and got the same results that even further confirms my thoughts
i posted in team upstate for you, but if you have not seen it
i am not from rochester but there are a few who are
if none of them can meet you i would test it for you if you sent it to me, i can tell you in 30 sec if it records on both channels or not
but you seem to know that already based on the ipod test
so actually if you sent me the adaptor that would confirm