I have this issue as well. I have adjusted my Harmony 676 remote so it defaults to the "DVD" input when I turn it on. However, when I want to listen to CDs it still defaults to the "DVD" input. I need to call Logitech and they will work it out for me. I suggest you do the same. I have issues in the past where I did not want a power on signal sent to my projector as I turn it on manually and do not let it run all the time. I called them and they adjusted the configuration accordingly. I have just been lazy on calling them to help me with the 990.