Audyssey is a not a fix all, it only attempts to equalize what it can within it's somewhat limited range and if the Audyssey you are using is an older version, it may well be killing the sub to equalize the room. Try running the system without Audyssey.
To further the idea of moving a sub. I found that simply rotating the sub within it's normal spot can help with the way it sounds. I went from straight out 90deg. from the wall, to facing the opposite wall at 45 deg., to firing directly into the side of the couch which was the best sounding placement.
