I'm having the same problem, but this seems to only happen when I am +listening to music from my iPod in iTunes+. Since the latest update, the music will pause or skip at random intervals, and eventually, it ends in me getting frustrated, trying to eject my iPod, and having to attempt "Force Quit" in iTunes to make it do so.
Of course, none of this happened until I got the latest update. My iPod is pretty old (third gen), but it was working with iTunes just fine until this past update.