Longer is quite common as it is not actually a distance measurement but a TIME measurement, and some subs have circuitry that introduces delay. But a distance setting that is less than the actual physical distance is wrong. Are you using a mic stand with a boom arm?
(switching over to iPhone under a palapa .. by a bar ... )
No, just the Audyssey mic on top of a box to get it at ear level in my listening position. I've never had it come up shorter than the actual distance.