I do notice a different subwoofer effect too. I had heard it is out of phase on the 6 channel bypass, compared to all the other digital and 2 channel bypass options. Is that true?
http://ubb.outlawaudio.com/ubb/Forum15/HTML/000701.html Yup.
Also, if you use 6 channel bypass with the 80 Hz analog crossover engaged, no double bass. If you do 2 channel bypass with small speakers, you get double bass. If you do 2 channel bypass with large speakers, no double bass. You might be hearing that too.