Thanks John. Sounds like you were right.
I also managed to find the "official" answer today from Home Theater Shack's Guide to using the BFD:
NOTE: Something that you should remember to do when you are setting up your BFD is add a foot to the value you enter for sub distance in your pre/pro or receiver set up. The 1 msec DSP processing delay in the BFD would account for approximately a foot in distance.
I seriously doubt adding 1' to the distance makes an audible difference, but I'll probably do it anyway next time I run Audyssey.
Jason