Call me. I'll pm you my number. I don't want to type out everything I'm thinking on my tablet.
1) why is your bottom end rolling off at 25Hz. Have you turned off your hpf filter and measured? Have you adjusted the hpf filter knob in real time while measuring with omnimic? Either your hpf is set too high or your subwoofer has a placement problem and needs to be moved. That 18Hz to 25Hz range is a lot of fun with movies and you are missing it now.
2) have you turned off all eq in the avr before taking measurements and adjusting with the omnimic and Mic2200? That is the proper order. Set up sub eq manually with no eq from any other source in the chain, then rerun room correction software like ympo, Macc, or audyssey.
3) level set the sub spl after every eq change. Make sure the spl is the same using the omnimic and your avr test tones. Some of the variances you describe May simply be that the sub is not playing as loud or is playing louder than the previous setting after the eq change.
4) daisey chain the two channels of the Mic2200, so you can get two parametric eq functions. Avr sub out goes to channel one Mic2200 input. Channel 1 Mic2200 output feeds to channel 2 Mic2200 in. Channel 2 Mic2200 out feeds to your subwoofer amplifier. You can use a cable like this to daisy chain the two Mic2200 channels. Product 4749 from monoprice.
Then you can give a little boost around 30Hz to help too.
PS. What is the yellow line on all your graphs? I may just be having difficulties with my android device seeing things but I can't tell what the blue and yellow line differences are supposed to represent on my small tablet screen.