YPAO isnt perfect, but it does an excellent job where it's truly needed. In my experience, ported subs can yield a different distance than measured, but you should keep the distance set at the YPAO setting. Keep in mind, the YPAO is measuring the time it takes in microseconds for the Sound pressure waves to reach the mic to calculate distance, and the mic doesnt lie!!! The same goes for channel levels. When it comes to speaker distances and channel db levels, I recommend using the YPAO settings.
As for the glitches? The occasional 'false-reverse', a non-preferred crossover, or manually adjusting the speakers from big to small to set to your personal preferences are obvious, simple, and easy manual fixes.
You should also check other settings to make sure everything is set the way you like it. IE.... Sub-out to both or 'sub-only', dynamic range(should be wide), etc, etc, etc....and stuff like that.