I would do as others have suggested and try turning off YPAO. Also, this is super minor, but I would re-adjust the distances to all be the same and set the center channel to small. The center channel shouldn't have as much bass as the towers.
As another poster noted, it looks like there might be some aspects of your room, acoustically, that could be throwing off the response. It's really hard to tell without seeing measurements, so I'm guessing here. Doors don't necessarily cause problems, but they could. An opening in a wall is a really good way to "let the bass out" of the room. It's actually a trick that is sometimes intentionally used to reduce the impact of a reflection in the room called the primary axial mode which runs the longest length of the room and tends to cause both a cancelation and boost in the bass that is very significant. It doesn't actually matter if the door is on the front of the room or back of the room, the effect is the same.
In any case, all of this is conjecture until we see what is going on.
When running the test tones, you said it sounds like the bass only comes from one speaker. Can you get your head near the speakers when it runs and see if the woofer appears to be moving on the speaker that seems to lack bass? Maybe even put your finger lightly on the cone to feel. If you aren't feeling anything, then something is broken in the speaker. If you are, then it's just an acoustic problem.