When I calibrate, I use the noise generator built into my Denon. I cannot select the processing mode during calibration. And I don't know why a manufacturer would permit you to do so. If you think about it, processing modes operate by comparing data from multiple channels, extracting ambience (time difference) information and then steering that information to the correct speaker. During calibration, only one channel is of interest at any one time so the notion of processing becomes moot.

Now let's get to your second point. I and numerous others that I know of on these boards have difficulty calibrating using their pre/pro's calibration system but no problem calibrating using an SPL meter. My Denon for example auto-calibrates every speaker (except the sub) to +12dB (maximum level) which is dead wrong. It's also a fact that the Denon auto-calibrated just fine many many times during my first three months of Axiom ownership. And I never had this problem with my previous system as evidenced by dozens of auto-cals.

I've been meaning to try resetting my Denon to see if this takes care of the problem. At least one other reported that resetting didn't help.