If you run Audyssey (or whatever automagic calibration routine) with the sub's gain at 90%, the AVR will compensate by extremely low output from the sub out(s).
You should re-check everything (settings in the AVR, and as mentioned connect useing the top sub pre-out on the AVR to sub's input 1), reel that sub gain way back (11-12 on the dial, higher than half way should be unnecessary), rerun calibration.