The Auto Set-up was a bit wonky for me as well, it wouldn't find/set my surround right-back channel, though it found the left one just fine (I swapped cables and speakers each time).

I unplugged my 950, plugged in my 990 used atuo-setup (then used the SPL meter and the auto was damn near spot on, except for the one issue). It sounded great right out of the box, I guess I got lucky!