jaramill and vtnzr, it's good to hear that this is not just an issue with YPAO. I'm guessing it's just strange room acoustics. jaramill, how long have you had it set to 1? The guy at Outlaw seemed to think this was a bad idea, and I'm not sure why.
cel4145, the YPAO in my receiver does have a sub eq. I haven't studied the manual enough to figure out how to tweak things manually, but when I go into the menu under subwoofer, it says "param, reset, edit, exit," but they're all greyed out. The graph underneath is small and you can't zoom in to see that details, as far as I know. There's another section that says "PEQ Data Copy" with Flat, Front, Natural with the word "manual" to the right. It tell you to hit enter to "copy," whatever that means.
In the PEQ Select menu, you can choose between manual, flat, front, natural, or through. When you choose manual, you can then go back up to the previous menu that was greyed out under subwoofer, but now is selectable. Under "param," hitting enter cycles between Band/Gain, Freq./Gain, and Q/Gain. When you select edit under Band/Gain, you can choose between 4 bands and adjust the gain up and down. Under Freq. you can move from 31.3Hz all the way to 250Hz. There are 10 points in this range you can move the gain up and down. With Q it goes from 0.500 to 10.080 with 14 points to adjust the gain up and down.
OK, I just figured out what PEQ Data Copy does. You can copy what YPAO already did, whether it's flat, front, or natural and edit it just as I described above. This also enables you to see the details of what YPAO actually did. (If I knew what the hell I was doing, of course!