I spoke with Steve at Outlaw a few times about this... for one thing he says you must set your crossover points BEFORE calibration. That helped.
Tone defeat ON helped tremendously, I was able to save the configuration. Outlaw needs to take another look at the autocal program and make it more accurate. Right now we're paying for a program that really doesn't work as advertised.

You know what made a HUGE difference? The Delay/Distance calibration simply adjusts relative phase of all your speakers. Go back to actual measured distances instead of what autocal suggests and while running a music DVD step the Center distance up and down until the "image" snaps into focus. Try it... (thanks to the folks at Genelec for that suggestion)

Just for giggles I made an attempt using a calibrated mic instead of the disc provided by Outlaw. A little better, but not much. Today my LFM arrives so I'll have to recal all over again.
Another fine afternoon shot to hell!

Gonk, How does the SMS "sync" to your mains, and is it really worth the extra $$? I have an outboard parametric eq already in-line between the 990 and my sub.