Setting all speakers to 60HZ did add a 0 db to the center channel, -2db to the surround right channel, & -1db to the surround left channel.

Speaker distances stayed the same.

Does auto setup have anything to do with the Surround Configuration screen?

Yes, I would like to borrow your SPL meter for verification. Thanks.
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Sony KDS-R60XBR2
Outlaw 990
5 Outlaw 2200's
L/C/R speakers: Outlaw LCR
L/R Surround speakers: Axiom QS8
Outlaw LFM-1 Plus
Sony PS3
Toshiba HD-A3 HD-DVD
Comcast 8300HD DVR
URC MX-850