So my little OCD on this took over this morning.
I closed all the doors upstairs busted out the Audyssey mic and went to town.
#1, 4" port open sub set to 1 port open as per HSU instructions and yes the valley was still there
#2 same setup and phase set to 180... oh my that was bad diped down to -18 for the peak.
#3 two ports open and phase @ 0 came out the same as #1
#4 both ports plugged sealed mode and it was a little better than #1
I have two Marantz Audyssey mic's and one Onkyo. I did the above with all 3 and still can't get rid of that valley or set my mains to small and 80.
If I get time maybe I will do something not to smart like cover the bottom speaker on the S60 or run Audyssey with my S20 and then see what I get.