My problem matches everyone else's, but with a little bit added. First, I should specify that this is ONLY when running through the multipin adapter through a USB plug. Headhphone jack does not do this. After a few hits of crackling sound as described by others, the audio signal cuts out entirely. I noticed two things though: First, although the audio signal doesn't play, the audio on the unit is still playing... that is, progressing through the track/podcast you were listening to. Second, if I toggle through the audio sources on my head unit (Pioneer DEH 7000 BT in a Toyota Corolla) and return to the USB source the signal is back. It will then stay for another 10 minutes or so, then repeat. It seems to repeat cutting out and going through that cycle in decreasing amounts of time until it gets to about 3 minutes... that is, playing for 3 minutes or so, then cutting out completely until I toggle through sources. This all started the day after the 4.1 update.
Apple, you're really trying my love for your products!