Audyssey attempts to determine if your speakers can handle low frequencies. If it senses that they can, it sets them to large and for many processors that bypasses the subwoofer by putting the lower frequencies to the mains. Go into the speaker settings and set the mains to small and then set the crossover frequency manually to somewhere around 80 hz depending on your mains. It shouldn't affect how Audyssey performs too much but it will let your sub do the heavy lifting and allow more power for your mains.