Sometimes different sources have different pre-amp voltage levels. For example, my Clarion deck has a 6v pre-amp signal whereas the Alpine deck he indicated has 2v pre-amp outputs. A higher pre-amp voltage allows you to set the amp gains lower. The ipod likely has a different pre-amp voltage than the deck (Full disclosure: I have absolutely no idea what the ipod signal level would be).
That being said, your later post about the subwoofer ON/OFF setting seems to be a very likely culprit as that wouldn't be present in the ipod signal. Not only that, that setting is probably so buried in the menus of the headunit that it would be extremely easy to miss. You've done some research!
Tincup has a pretty kick-*** car going - it deserves some serious tunes as well! :rock:
