Drew, your second post in which you apparently indicate that even with the M60s handling the center in "phantom" mode, the center was disappointing, suggests to me that there was merit in Mark's comment, although you tended to dismiss it. The Bose may in fact be producing a unrealistically bloated response in the upper bass frequencies, which may nevertheless sound impressive to you.
You haven't heard from me that the auto-setup is no good; my view is that it's at least as accurate as the result from using a separate SPL meter and making adjustments manually would be. In any case, if you're calibrated at least reasonably well(but check the polarity anyway), that along with the M60s "phantom" try indicates that the problem is likely to be with the Bose.
