The YPAO is working, it sets all other speakers but the sub. I sent an email to SVS and they said it might be because the sub has a delay to turn it on when it receives a signal so it will go into standby when no signal is present. To get past that I should make sure that delay was turned off and the sub was set to always on. I did that and when I ran YAPO again it still did the same as before.
When i set the sub manually it plays but I would like to haveYAPO adjust to match all the other speakers like it supposed to. No tone comes from the sub but does from all the other speakers.