Try re-running set-up again. Make sure the PB-2000s phase is set to 0 and the low pass is set to LFE (full clockwise). Also, are both subs on the same wall?
Carefully level match each subwoofer to exactly 75 dB per the Audyssey set-up. If you do this, the overall subwoofer channel level should come back in the negative range for both subs.
Also, leave the mic at head level only at the primary listening position. Run it 3X without moving the mic and then move-on and save the results. I suspect one of your mic locations has a bad null and Audyssey is attempting to compensate for same.
After set-up runs, make sure all speakers are set to Small, then set all crossovers to 80 Hz (unless Audyssey set them higher), set the subwoofer mode to LFE and set the LPF/LFE to 120 Hz.
Report back with the post-Audyssey subwoofer channel level set for both subs.