Alot of great answers above, if one of these do not answer your question, its possible a speaker problem. To put this all together, Start easy, check your speaker wires at the amp and the speakers, + to +, - to -. Next, temporarily move your speakers closer to the walls/corners, see if this brings out the bottom, next, you might want to slightly back your mid and treble controls down a hair on the back of the speakers.
My guess is as mentioned you are dealing with room nodes. You might want to do something like measure the room and use something like the "Golden Triangle" formula by Cardas for imaging. Placing speakers by its measurements do help get rid of room nodes. I suspect that you have gotten used to a bit of bass boost by your other speakers being closer to the walls. You can use the Golden Triangle, then if not enough bass, start moving your speakers, by a couple inches at a time toward the corners until bass reinforcement is where you want it, then adjust your tow in accordingly. I hope all of this helps. Tim
