Hee, hee. Pioneer players do the same thing, and everybody thought it was Pioneer's fault.
But it's not. It's a stupid incongruity between DD/DTS where a 10 dB boost is applied by any processor, vs SACD/DVD-A where it's not.
Here's what I did: In your processor/receiver, purposefully set the sub level about - 5dB from the speakers. Now, adjust the sub's level control on the sub itself so that you get the right numbers for DD/DTS. Now, if you adjust levels on the Yamaha, you should find that if you have the sub adjusted to about + 5dB compared to the rest of the speakers, you are golden.
Switch it to SACD mode, then go into the setup menu. Its explained on pages 31 and 32 of the manual and is a bit detailed for me to explain here. Each increment on the speaker adjustment for SACD is 0.5dB.
John, the test tones and such for SACD are pretty stupid. Its indicating that it puts out a tone via the mains and the sub so you can adjust the sub level. It makes no sense whatsoever. The manual says this for the right rear speaker level adjustment:
Select BALANCE RS, then press ENTER. The unit displays the following indication, and the left and right main speakers and the right rear speaker output a test tone at the same time. L/R - - - + - - - RS
Moving the slider left and right adjusts the volume of the right surround and does nothing to the mains. Now why anybody would want a test tone out of three speakers at once I have no idea. So choose Balance SW and adjust it. Unfortunately you'll have to do it by ear because its just not real accurate.