I had this exact problem with my Bose Soundock Series II. I called Apple Support. At first they tried to blame it on on Bose, but after I got to a senior tech rep, he offered the following solution that fixed my problem.
In Settings on my iPhone 4s (that I unfortunately "upgraded" to ios6 -- big mistake) I went to Settings, then General, then Reset, then Reset All Settings. This will shut down your phone (so I dropped the call with the tech support guy). Then I powered it up. My screen background had changed, and God only knows what else. But when I played music on my iPhone 4s, then plugged into the Bose Sounddock, miraculously it started working again as before.
You might want to be more cautious than me about the "Reset All Settings", since I still don't know if that did other damage, but it did solve the Bose Sounddock problem. I hope this works for all of you out there.
I am pretty appalled about Apple's non-reversable "upgrade" strategy, and there apparent lack of concern for all the things they break in a user's home eco-system when they cavalierly push out updates. There was no warning about what might change or break, and no return path, and not a lot of apparent concern at the corporate level. Fortunately I found a guy who offered the equivalent of the classic (try rebooting) solution. Fortunately this worked, but I have no doubt that if it hadn't, the answer I would have received from my "friends" at Apple (who oh so care about us consumers), is that I was out of luck, and the thousand bucks I spent on three Bose Sounddocks for different parts of my house (which I bought at the Apple Store!!) was just down the drain. Nice guys those Apple folks.
The particular tech rep I got was a nice enough guy, so no complaints about him, it's Apple's overall arrogance and lack of concern for me as a consumer that I find loathsome.
