Very odd indeed, looks like you are getting some sort of cancellation going on only when eq is engaged. Can you plot just the sub and then just the main speaker response?
Also, if you are setting levels based on receiver test tones those do not run through audyssey. I'd recommend leaving them as they are at least for now, and if you change them used a calibration disc for the tones.
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You say "... if you are setting levels based on receiver test tones those do not run through audyssey". The Audyssey calibration actually sets the speaker trims, and the level of the test tones is indeed affected by these trim settings. So, what exactly do you mean?