Weird

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.) 

Maybe plug it back in and then unplug the other one?
You’ll have an extra data point at least…

There are leads to reverse, but they’re a bit of work to access. Remove the cap/top and take the sock off. This will allow you to access the connections for the sub amp. If I can do it, it’s not difficult. Hardest part is getting the sock back on the same way it was from the factory. 

RVpiano is like any RV, he keeps on trucking.

IMO, the usually level headed Jason is wrong here…do not attempt to disassemble the speakers!  Newbee is on the right track.  This is about room interaction and too much low bass energy when both active woofers are powered up. Try reducing the levels by a lot on both to see if you can get back to the same overall bass performance with both working as you have with one turned up higher. If you succeed with this you should benefit from lower distortion and more uniform response across seating positions.