Thanks, Otto. I have a seperate preamp, an Outlaw Audio ICBM (I just use it for bass management because I have an older preamp/pro:
http://www.outlawaudio.com/products/icbm.html, and a 5 channel amp. All of the channels from the preamp go into the ICBM then to the amplifier (and the sub) and out to the speakers. Here is the setup for the signal from the computer (output). I ran the output cable from the computer to the left channel of the inputs of the preamp. Then I ran the left output from the preamp to the channel that I am testing (input for the ICBM) For the graph I show in the first post, it is the center channel which includes the sub.
I have a Def Tech Super Cube II subwoofer. When I did the sub alone (as you suggest by just unplugging the speaker wires) I get a pretty big hump from about 30to 50 Hz (at least I think it's from about 30to 50 Hz - my files are on my home computer). I will go ahead and post that later today. When I connect the speaker it settles down like my graph that I have posted.
Is the drop from 30 Hz unusually steep?? When I tried adjusting the phase the dip from 50 to 60 Hz just got deeper.