I'm certainly no expert, but here's my $.02 - I agree with spiff, 3:00 sounds awful high. Not sure the size of your room or the amp. I can't take my VTF-2 past 10:00, maybe 11:00 without some distortion. Is your sub output level reduced significantly on the receiver?
I tried those test tones with the HSU disk, but really didn't get anywhere. The AVIA test disk really helped me because it showed the exact frequency of the sound on the tv as sweep went from high to low. I'm sure some more knowledgeable folks can chime in here, but my room has some pretty severe bass humps that would jump 20dB at certain frequencies. Maybe the music you're using is heavy in a range that activates some room nodes you have which exaggerates the bass.
