Just came from the Apple store, told the same story to one of the guys there who use to work in a recording studio. He knew what I was talking about. Now I've talked to Apple Care twice, Bose once, no answers. But this guy suggested a USB device, like an iMic which I happened to have so I gave it a try and so far, NO POPPING. I have my fingers crossed, but it seems to be working. I have the speakers plugged into the iMic, the iMic plugged into a USB port.
Bottom line, this is screwed up, I shouldn't have to do this work around. Apple has to know about the problem. But until they own up to it at least now I'm not going nuts with this noise. At least I hope not. I'll post again if I'm wrong.