It sounds like the YPAO thought that it needed to attenuate all of your front, center, and surround levels, in order to get enough relative subwoofer volume to "balance". (I am guessing that your receiver is limited to boosting the subwoofer signal to +9 or +10 dB, and once it did that, the only option to deal with too little sub-woofer output was to lower all of the other channels.)
Two possibilities suggest themselves:
1. When you ran YPAO, the sub-woofer's own level adjustment knob (on the subwoofer itself) was set too low, so that YPAO needed to raise the signal to the subwoofer too much. Try putting the knob on the subwoofer to a higher volume setting, at least "half-way", or maybe even a little higher, and then re-running the auto set-up.
2. Possibly (but less likely) you have a phase issue with the sub-woofer. Try reversing the sub-woofer phase (should be a manual setting to do this), and then re-running YPAO.
I am betting on it being number 1, above, as the most likely culprit. An alternate method of fixing it would be to return all of the speaker level adjustments to 0, and then use manual test tones to manually set the subwoofers own volume knob so that it sounds about balanced to you. Then you can consider re-running YPAO to do fine adjustments. The basic root cause is that there are two volume adjustments for the subwoofer - one done inside the receiver, and the other done by the knob on the subwoofer. One being too low means the other needs to be too high to compensate.