Help! unwanted "flanger"

[seamonkey]

Each of those Mic's has a different response curve that can be contributing to your issue. Take a look at your second screen shot and you can see the differences in the wave forms.

You're probably also getting some reflections off the wall on the right, the ceiling and what may be in front of the cab.

Like Seamonkey pic the Mic track you like the best then You might try re-recording with that Mic and a direct track to blend into the the mix.

You have the luxury to keep trying different things without paying by the hour

Record and enhance, not record and correct.

I think you got it.
http://www.realtraps.com/video_comb.htm

 

[Ajak]

Interesting video, thanks! But neither the cab nor the mics were moved, so why does the filter sweep?

We tried to avoid as much reflection as possible. We put some acoulstic foam on cases facing the cab (I have no picture of that. The ceiling isn't parallel to the floor. The wall on the right however could be too hard.

 

[seamonkey]

Could be the guitar player moving around in the cube space - sound reflecting back to the mics.
Could be the cab on wheels rolling a bit, or the guitar player pulling the chord and shifting it's position. It's a mystery.