I haven't been able to use auto-calibration with my current subs (18" Electovoice in 13cu cabinets and Adcom 555a). The sensitivity is so high that the white noise is at around 112db and the 990 won't recognize the subs as being present. Any suggestions as to how to overcome this problem? I've setup the subs manually after calibration is complete as my solution for now.

I think you've already found the workaround - do your calibration maually.