David, the auto-calibration setting using the Audyssey measurements isn't literally a distance measurement, but is a time measurement of the delay before the signal reached the microphone from the sub. Besides the actual physical distance delay(about 1 millisecond per 1.1' distance), filters and/or DSP processing in the sub also create delays of varying amounts. So, a difference in the "distance" result from the actual physical distance is no cause for concern, and should be left as was measured.
