If I correctly remember a post from Scott recently, the information displayed during auto setup shows how much above or below reference the channels are. That means that a "+5dB" reading would require a "-5dB" adjustment to achieve reference level, which matches with the -5 and -7 settings you mention.

I'd suggest two options. One option is to use the 990's internal test tones and your meter to check out the channel calibration settings by setting the 990's volume to 0dB and going into the channel calibration menu. That will let you double-check the auto setup. Another option is to simply adjust all of the channel calibration settings (except perhaps the subs, which I tend to adjust by tinkering anyway) by the same amount (perhaps increasing each channel by 5dB so that the surrounds are near a 0dB trim setting).