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