Both.
The first sign of a bad HDR (or reason for over-processing) is a lack of tonal range. This comes from not shooting enough exposures, usually because people rely on the exposure bracketing feature of their camera and only use the 3 shots. What if -2 (or -3 depending on your camera) isn't underexposed
enough? High contrast scenes often require much more under or over exposure but the most important thing is to shoot every whole stop in between (ie -5, -4, -3, -2, -1, 0, +1, +2, +3 & +4). That way you get smoother transition between tones and a better range of luminance values as well.
If you shoot like that, you don't have to push Photomatix so hard to get the full dynamic range covered so you introduce less noise and you get much more natural looking results.
You can still over process though. I post these as examples only (they are not my work). Neither look real. Both are horribly over processed. There's halos and noise everywhere.