I doubt that the inversion of absolute phase has anything to do with your problem. What strikes me as possible though is that with both subs running perhaps you are just getting too much bass and this excess bass is muddying up your upperbass/lower mid range. You have a bass control on the back of each speaker. Play with this for a while, starting out with minimum bass on each speaker and increasing it until the bass can be heard/felt - you might do this one speaker at a time - perhaps because of your set up/room interface only one speakers location is problematic. From your pictures nothing is obvious re room acoustics, etc. (Except they appear to be on the long wall - in my experience speakers usually sound better on a short wall firing down the long dimension of the room. (Think shoe box type concert hall.)
Weird
I have a pair of GoldenEar Triton 1 speakers, which have built-in subwoofers. Evidently, the right subwoofer lead fell off the speaker some time ago without my knowledge. I’ve been listening for quite a while with only one subwoofer, really enjoying the sound in blissful ignorance. Everything sounded great including pieces with deep bass such as formidable organ recordings.
Today I discovered the plug out of the wall and plugged it back in. The system immediately closed up, became dull, lacking ambiance. I pulled the plug back out. Sound was wonderful. Everything sounded just right, including the bass which was full and rich.
I’m now listening without the right subwoofer for good.
Weird!