As you're discovering and others have pointed out, sound waves are fickle things and small changes can produce big changes. Especially with the low frequencies that the sub produces. I bet an hour or two doing a 'sub crawl' would help out your situation.
In my den/theater room, if you stand up in front of the couch near the center of the room, the sub doesn't really even sound like it's working. Conversely, if you go stand right next to the rear wall, near a corner, you get an enormous amount of sub - far overpowering to the mains. But from our seats it's all balanced appropriately.
Go rent
Master and Commander and play through the opening naval battle. Crank it up. If the pounding of the cannons doesn't knock your socks off, then something is wrong with your setup.
