Thanks all. These are very helpful suggestions and thoughts. Richard, I do indeed have a spectrum analyzer -- I have the PC based one from XTZ, as well as the Velodyne SMS-1. You point about built-ins shelves is very interesting -- my room has built in-shelves (housing CDs) all along the longer axis and this is the axis and the side of the room that the speakers are placed with.
Shadorne, that's very interesting about the subwoofer. Mine is side firing unfortunatley, but I could try angling it down a bit. I guess I am lucky that it the null is definitely narrow bandwidth -- I don't have it in front of me here to report back but it is definitely not a wide band problem.
One question: when you look at the results of the websites that analyze the room, how do you know what will be a null and what will be a node?
Thanks again, all.