I am glad you are able to tell the difference with different sources. I have the same/similar issue. Audyssey set my center to 80 and left,right to 120 with surrounds at 100. I have tried manually setting them all to 80hz but I cannot hear the difference between the 80 and 120.
Your case is somewhat different, because the gap (if any) between the 120Hz setting that Audyssey determined, and the 80Hz that you set, is much smaller. Most subs will continue to have output at 120Hz, so I would recommend keeping the 120Hz crossover for the mains. JMHO.