I know Zone 2 requires an analog input. I've never used the USB input for the 990, but since it's not analog, I believe that's your problem.

The requirement of using an analog input for Zone 2 is a very common one. I've played with three or four preamps (all very nice) and all had this same requirement. I'm sure it's because of added design, parts and manufacturing cost for a feature that relatively few people use. There would be at least one more two channel DAC involved, as well as added digital circuitry.