My experience with the 990 auto calibration has been very disappointing. The delay calibration seems to be ok but the surround levels and sub level have never been right. It's important to set your speaker size and crossover BEFORE running the test and to make sure the tone defeat is ON.
You're better off using an RS meter and the 990 generator or the AVIA test disc.
Also, see my post about 990 bass level problems.