fader8,
Getting to the bottom of this might reveal something interesting about one or both of these equalizers. Are you game?
Normal scientific method would be for someone to try to replicate your test and show the same result. Unfortunately I can't help, since I own neither Logic nor Waves licenses. So I suggest that you try some different test methodologies to see if the results match.
The tone bursts you used are rectangularly windowed, which means they are causing a lot of spectral splatter. To control this, you could use a more gradual window. Common choices are Cosine and Blackman windows.
Since you are good at making two-channel measurements, how about making a direct comparison between the Waves and Logic linear phase eq's (set as in your previous test) to verify that the difference curve is indeed flat?
Next step would be to measure the impulse responses of both products and compare the results. I don't know if spectrafoo can do this, but
ARTA can.
David L. Rick