It could also be the source material you're listening to is mixed that way. When doing my post-auto-calibration manual tuning, I utilized multiple sources when fine tuning my system to matchup the volume, character and quality from all the channels. One item was a quad-channel music disc of Pink Floyd's Dark Side of the Moon. The center image between the right and left speakers were slightly tilted to the left and when I rebalanced it to the center, it threw off every other multi-channel item as well as 2-channel music CD playback.
While I do agree that auto-calibration is good at setting things that humans can't detect reliably like phase & standing waves without special equipment but they still aren't perfect at it and there is no doubt that my manual re-eq does a much better job at getting all the channels to sound more similar. I've swapped back and forth between my re-eq preset and the original auto-tune preset. My adjustments are much closer to sounding balanced on tone and also the sound pans around the different channels with no audible difference. It's a clean, consistent panning. This is one of the big reasons I love Pioneer;s MCACC. Also, from just a pure auto-tune perspective, MCACC also sounds the best to me after I did my own head to head comparisons with Harman's and Audessey's auto tuners.