I did a quick search and found one from Gene:
http://www.audioholics.com/reviews/receivers/yamaha-RX-Z9/auto-set-up-and-ypao-configuration
In the "Distance Check" paragraph he said something about the sub's large wavelengths, room.. etc. I guess that's one reason why it helps if you disable the LP filter during the auto cal process. I also suspect YAPO may not be as accurate as Audyssey in distance measurements. Basically subs are a bigger challenge for auto cal system to figure out the distance. No big deal as you can always punch in the physically measured number.
That being said, I don't you how far off your sub is, mine is within a couple of inches and we both have Audyssey XT. If 24.5 ft is say a few feet off the actual physical distance then I suggested you do it again but make sure you follow Audyssey instructions to the letter, such as ensuring a noise floor of <45 dB, using tripod, disabling LP filter etc.