The difference is the room, where you sit, where the speakers sit, and the placements of treatments (or lack thereof).
Anyone who is versed in acoustics will say that over half what you hear is the room itself. The answers might only vary in that some say it's a bit over half what you hear, and others will say it's upward of 80% of what you hear.
Common culprits might include being too close to rear wall as a listener, sitting in a bad null like mperfct suggests, having speakers too far apart, having speakers too close together, having them too close to side walls, having them too close to front wall, even worse being too close to both side and front wall (corner), and then the worst of all is just having a terrible room (perfectly square for instance).
In any case, when you said, "The only differnce is that they were using an separate amplifier to power the speakers . . .", that is not true, and I wanted to clarify that.