How far is your listening position from a room boundary? I had a similar problem in my room if I was <4.5 feet from the rear wall. When I moved my chair out into the room the problem went away. Also how close to a room boundary are the speakers? One thing that helped me tune all of this in my system was to get a Radio Shack SPL meter and a Stereophile test CD with test tones. I had booms at 40-50 and 125 and suckouts at 70-80 and 160Hz.
My $0.02
Aaron
My $0.02
Aaron