While room acoustics are, for the most part, a matter of physics - Sound acts predictably in a given environment - listening to music is a very personal and extremely subjective thing. Room acoustics in the home environment are a good example of this.
In recording studios and other sound-sensitive environments, we take great care to dimension, shape and otherwise design the rooms so as to work with, eliminate and/or control acoustically harmful manifestations, such as adverse reflections, low-frequency build-ups and inadequecies due to room nodes, standing waves et cetera. Conversely, in the home we are stuck, more often than not, with bland rectangular spaces, not unlike boxes, in which to create 'our' perfect soundstages.
One of the first considerations should always be: How will sound react in this room? In short, how will the room be involved in the reproduction of the sound coming from the speakers? Will the hard, reflective surfaces of the walls, ceiling and, perhaps, the floor adversely color the mids and highs, causing acoustic 'smearing' - a lack of definition due to multiple and overlapping, uncontrolled reflections - and the inability to locate sound sources correctly? Will the physical dimensions of the room cause an unwelcome reinforcement of the lower musical registers, affecting low-frequency definition and uniform bass extension? What can be done to improve and correct any anomilies?
In acoustical design in the home, as in recording studios et cetera, there are two major, and different, areas of concern. Environmental Acoustics addresses how sound will react in a given space/environment. The second area, sometimes referred to as Boundary Acoustics, deals with how sound will transmit to other areas of the home or building, be it through the air, through the HVAC ducting or through the structure of the building itself in the form of leakage through walls or floors and/or vibration. Boundary Acoustics are, I think, a discussion for another time.
There are many books available which will give a lot of helpful information and suggestions for people who want to do it themselves. Alton Everest's "Master Handbook of Acoustics" is one of them. For others there are companies and individuals who specialize in design and acoustics.
Ht802, it sounds like you are having the most trouble with reflective surfaces? Experiment by temporarily hanging heavy blankets (or some such devices) on the various walls and auditioning the effects that they have on the music that you are hearing from the speakers. If possible, try and minimize the 'liveness' at either side of you listening area. This will tend to dampen and eliminate the secondary, and definition occluding reflections arriving at your listening position.
The idea is not to have a 'dead' room where there is a lack of excitement, no (kinetic) energy. In rooms such as this the music tends to sound thin and brittle and, to me, lifeless and uninviting. Rather the ideal is to have an environment where the room is involved in the reproduction of the sound in a complimentary and pleasing manner.
This is were room acoustics come in. Even the distance that you place your speakers from the wall can have a, sometimes, significant effect on how accurate and smooth your bass response might be. For instance, you say that you have placed your speakers 48" off the back wall? If this measurement is from the wall to the front of the speaker then you can expect a dip near 70.5Hz (more accurately 70.625Hz). This is because if a speaker is placed 282.5Hz (4'- 0") from the front wall there will be a predicted frequency dip at near 70.5Hz. By way of explanation: Sound travels 1/4 wavelength to the wall, bounces off and travels 1/4 wavelength back and is subsequently 180 degrees out of phase (1/2 wavelength) with the direct signal at the front of the speaker.
Of course, if it all sounds good, who cares? Let me know if I can be of any further help?