Wow, found this excerpt from June:

"There is a bug with both old and new firmware ... If the Tone Defeat is set to OFF, there is 6dB (or more?) difference between the fronts (fronts are louder) and center channel when calibrating with internal noise. If Tone Defeat is ON the unit calibrates fine.
Anyway, see if you are stepping on this bug. "

The internal noise referred to was with manual tones, so I guess I may indeed have found this same bug. Will check tone control tonight...