From the "been there, done that" camp:

The 990 zero's the left front speaker, and callibrates all of the other channels relative to that. If you run a mix of balanced and un-balanced signals (I've done it, it works fine), to get the wide adjustments required you may need to set the left front to something other than zero.

For example, lets say you run the mains balanced, and everything else un-balanced. You may find that there is a (making this up) 20db difference between the mains and sides. Auto-cal only allow +/-15db deviation from the left front; which is automatically set to zero. So, the 990 can't get enough gain for the side channels.

In this case, you would need to manually set left/right mains to (for instance) -10db, and the sides to +10db; which will get the needed 20db differential.

This can only be done in manual mode.