This is going to catch some flack from the Audyssey Lover's Association (TM) but:
Any 'room correction' program that ignores room dimensions is nothing but a glorified auto setup program! Sure, it's convenient to not have to input distances (delays) and crossovers manually, but as you've seen, they are not 100% reliable.
http://www.aes.org/e-lib/browse.cfm?elib=17839 Dr. Floyd Toole paid to make this paper public. He explains to the n'th detail the physics on why an omni mic situated in a room with unknown dimensions only offers part of the story, and shouldn't be used as universal remedy for small room acoustic 'problems'.
To my knowledge, only the latest Harman processors allow for this, but they are extremely high end! (whose development was orchestrated by Floyd's successor Dr. Sean Olive)
Save your money, and move your speakers! Experiment with the distance to the wall behind them, as well as the distance between them. Adjust your 'Auto-Eq' settings accordingly.