The first (and only) time I've run Audyssey with my new Denon avr, it seemed the sub was a bit low also. I just turned it up a bit on the back of the sub. The next time, I'm turning the sub down a little more before I start the Audyssey program. Then I'll try the +3 for the sub. I had to do a +4 for the center.

Funny, because I never had to do any of these special adjustments with MCACC and it always sounded good to my ears, without any further adjustments, other than setting L/C/R to small.