Crow, no I haven't plugged my phone in for any update since it's launch (it has iOS 5 and there haven't been any updates). That's why it doesn't make much sense. I do testing of hardware for my company routinely when it comes to bugs reported in various hardware or pieces of software, something like that would have been my first thought so it's definitely an odd situation.
The only thing that I can assume is that when playing the iPhone (the song was downloaded through the iTunes app) through the iPod input (not going straight to Pandora) that it either updates a setting on the phone or recognizes the cable/headunit in a different way or category of peripheral (to allow pass through of audio/video rather than just a charger). This is what I don't know since I'm not familiar in that level of detail of how the code is written for integration of these devices with Pioneer(or any) headunits. I had the iPhone 4 before the 4s and it worked flawlessly, and the 4s is working just as well now (pending my test of the MotionX app as well).
Back to the updates idea, I still can't remember if Pandora (or Rhapsody) came out with an update since launch. Would that have affected it? Don't know, depends on how the coding is I guess but I'd be surprised if it would be coding at that high of a level that would make the device recognized.
It seems that every day more and more detail on this is coming out, but all I know is it works for me and I was going to raise **** if it didn't (bought my radio 2 months ago).