Hey Adam,
Thanks again for the response. I went and bought some new cables (digital audio, optical, HDMI, etc...basically the works). I did only have it connected with an audio cable (left and right, my DVD player also has a Sub out, would that make a difference, I have no idea where I would even plug that into , in the back of the amp). As far as the reverse polarity with the speakers, I do find it strange, they are connected correctly, and with the rear surrounds connected, i now have a front that is reverse polarity, if I remove them, the front is no longer reversed? I did hear sound coming from all speakers though during the auto setup. Maybe something is wrong with the amp...I may have to call Yamaha. If anyone has any ideas for me to try, I would really appreciate it.