When using an SPL meter, you are measuring white noise with all the room problems. When Audyssey measures, it uses sweeps. Also, there is a +/- 2db variance on the SPL and the Audyssey MIC.

The sub distance is a problem. It should not be closer (it could be farther and still be correct). Was there any room noise when you did the test. Thinks like cooling fans can make Audyssey give weird results.

Dave
Audyssey Setup Guide