i'm new around here as well, but i have a similar setup so i thought i'd add my 2 cents. i was messing around with the e7 and e9 when i first got them and had connected the e7 to my computer directly via usb, and taken one of the headphone outs from the e7 into the aux in on the e9 (effectively using the e7 as a dac/preamp and using the e9 as an amp... i was testing to see the difference and also if i liked the bass boost... suffice to say i found i much prefer the e7 docked into the e9!)
when i was done having my fun, i re-docked the e7 into the e9 like normal, and i only had a left channel in my headphones. i turned everything off, un-docked it, still only one channel. i plugged the e7 in directly via usb and plugged my headphones into it and they were fine, both channels. eventually, and i have no idea why, i plugged my 1/8th in cable back IN to the aux in on the e9 and unplugged it and i magically had both channels back.
i guess my advice is... try stuff and see what works. even if you think "this can't possibly do anything..." you never know.