OK try this:
- make sure all your speakers are set to small, set the crossover to 80Hz
- run the Yamaha YPAO auto setup, but set it to skip the step called "Speaker Size" because the receiver may decide that your speakers are LARGE which is no really the case (shame on you Yamaha for programming it like that). Actually, you can also SKIP the step for "Wiring" and "Distance" too, because your receiver did those steps the last time you ran the setup. In my receiver, I actually found the receiver autosetup WANTED to set my center to LARGE, but it stopped doing that if I skipped all the YPAO steps except "Levels" (and "EQ" on mine)
Try it again, if the sub still does not turn on, go up to your sub, and turn DOWN the volume(level) control on your sub by a 1/4 to 1/8 turn, and then run the auto setup again. If it's too low, your receiver will abort with an error, so turn it back up.... but if it completes the process properly, test to see if the sub is turning on automatically now. Also, confirm that your center channel is still set to SMALL.
I was finding on my sub that the receiver was not sending enough of a signal to activate my sub, so I turned down the level on my sub, and then the receiver is forced to send a higher voltage signal to my sub, thus activating it more easily.