I run into the same problem with mine and my DSP, really only when sitting outside of work. I turn off the bluetooth, back on, and then it's normally good to go.
Doubt it. Mine does it with an AMAS, which has nothing to do with the analog inputs. And also some songs will skip, and then not skip if i play it again immediately. I'm still guessing quirks with iOS, because it did not do it prior to the recent iOS update.The skipping part on the iPod part of phone was because the Dsp was sensing clipping and shutting the unit down.