Well, one thing is obvious from this graph. If you could set your speakers to "medium" the sound would be great
Seriously, it looks like the sub is not receiving signal when you are set to "large", ie the bass rolls off where the M60 rolls off, doesn't go any deeper. Is that how your receiver is set up, or is the M60 putting out a higher bass level than the sub ?
EDIT -- I don't suppose you could post a crude sketch of the room layout (doors etc..) so we could move your equipment around for you ? After staring at the graph for a few minutes the first thing that jumps out is that (as you mentioned) minimizing interaction with the walls seems to be a particularly good thing in your room.
First thing I would try is sticking the left M60 on the far side of the equipment alcove (nice setup there by the way) and shifting everything to the left a bit. Don't have it exactly centered on the wall but pretty close.
If that doesn't work for some reason is there another wall you could use ? At least all the walls are the same size...
In case you are starting to despair, you are doing exactly the right things here. A massive amount of testing and thinking, coupled with a significant amount of reading and discussing, resulting in some small, non-obvious change which in hindsight you can't believe you didn't try before
