Joe, as to difference in the level readings, as I've commented before, there's no good reason to believe that the SPL reading taken with a separate meter(and with human error in reading it possibly a factor)is more accurate(or as accurate)than the result from the Audyssey microphone and built-in meter.
Where the sub difference is shown as being significantly shorter than the actual distance, this would seem to indicate that a nearby reflection is affecting the result. If you had the microphone positioned clear of obstructions for the first central reading, maybe you should try another first reading from about 6-7' away from the sub even if not in the listening position , to see if a similar short measurement results.
