I've actually had issues with 990's test tones in general, whether using auto calibration or manual. My left and right surrounds calibrated with an SPL meter to +7dB and +9dB respectively while the left and right mains were 0dB and +1dB. This was surprising since my surround speakers are only a bit smaller than my mains and are about the same distance from the listening spot.

When I used the THX optimizer on one of my DVD's to balance the channels, the surrounds calibrated to -3dB and +0dB while the mains remained the same.

I ran with both setups for awhile and found the latter calibration to be much more balanced and natural than the former.

So, based on the experience I had, I'd echo gonk's advice and suggest you just calibrate manually.

As for the difference between the S&V disc and the 990's test tones, it seems reasonable to expect that different source noise could yield very different results. That was certainly my experience, and I've read similiar stories from others who compared different calibration discs to one another like Avia and Video Essentials.

Obviously, the only way to tell what's right (assuming one isn't wildly off) is to just try both configurations for awhile and see what sounds best.