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I did not turn off my mains because a 50hz crossover would limit these results.
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I don't really understand that. If you shut off the mains and do a sweep to 200Hz with the sub only it will separate where problems lie between the mains or sub. Since the sub is the only device to receive equalization, it's the starting point. Do a sub only sweep and use logartithmic graphs (press the little ICON button at the top right hand side of REW called Freq Axis).
Once you have equalized the sub, then add the mains and work on the crossover transition problems that may arise. That is likely the problem dip at ~60Hz in your plots. Adjust the sub phase control to reduce that peak. It is likely a result also of having the mains set to large. Usually small is a better choice.
As John says, you're clipping your signal into the soundcard. The results are not useful until you solve that level problem.
Look at the SCOPE tab and you'll see the clipping after you've taken a measure.
In the SCOPE tab, the smooth sweep is the output of the soundcard and the dark red envelope is the input to the soundcard with the Y axis is the percentage of digital full scale.
Here's a SCOPE of a normal sweep. See the dark red does not hit the light red.
SCOPE full no clip.jpg
If I expand the vertical scale I see a nice input waveform of input and output signal of REW.
not clipped.jpg
Here is what it would look like with the signal clipped - not good.
clipped.jpg
In the impulse response the harmonic distortion components appear as additional impulses at negative time. You have a lot of distortion showing. Do a cable only loopback measure to see if your computer and soundcard are contributing to this problem.......
brucek