Yeah, good job on the graphs......
You need to turn off all the other speakers and only check the response of the
sub by itself, using the crossover frequency you would normally use. That means, using the CD or AUX input to your receiver, and then put the receiver in stereo (that way only the mains and sub are on ). Then disconnect or turn off the mains. Then do your REW check levels etc and do the response. It will reveal a lot more than what you have now. I suspect a lot of the problem will be that the mains are a lot higher than the sub in level....
Maybe post another plot when you've done that....
brucek