Toby,
Your description of what happened when you set the M60s to "large" (with the sub supplementing below 60Hz) does make sense. It seems that, by driving the room from three separate locations (FR, FL, and Sub), you are canceling out the big room-mode dip at 40-50Hz to some degrees. So, maybe this is a good starting point for you for further tweaks.
The different peak frequencies you observed between the FL+Sub and FR+Sub sweeps are nothing surprising. Are these peaks seen with the M60s set to "large" and the sub added below 60Hz? Anyway, this strongly suggests that it is worth playing around further with the placement of the M60s as well, since your major room-mode peaks are above the sub frequencies.
