Check the following:
1) Is the cable pushed in all the way into the iPod? If it's not pushed in all the way, you will only get one channel
2) Is the AUX connector correctly aligned with the BS9000's AUX port? You're not supposed to able to connect them except as designed, but I have a cable (from B&O) that doesn't have the little nub that guarantees that you can only insert it with the correct orientation. You may have the L input connected to pin expecting the R input (and the R input connected to an unused pin). You could test this if an iPod has "balance" controls: try setting the balance all the way to L and see if there is any sound. If there is sound, then the iPod's left channel is connected to the BS's right input. Try rotating the plug a little (clockwise, I think) and reconnecting. I sure wish it was easier to get to the BS9000's ports!
3) If you're using 2 cables (DIN to RCA, RCA to mini-jack), make sure all the connections are fully seated.
Stan