See if the following thread helps at all
The biggest issue for me is, the Bose isn't actually a true subwoofer but in reality, a bass module. So you might have to futz with a few things on receivers like the Pio, etc.
Have you also run through the other settings for various speaker types? I see the important stuff on p.30 on the manual here:
Also, have you tried the 'plus' setting, mentioned on p.31/left column?