I use the Photomatix plugin but make no claims on expertise. Sometimes "bad" results from Photomatix are often a result of using extremes in the settings. Try the default settings as a reference point. That said, sometimes those extreme settings give the unique look that you might be seeking.
If the scene does not really require HDR then forcing HDR may not yield a desirable image. Take a close look at the histogram of the "best" exposure from your bracketed shots. If that histogram does not show a lot of underexposed areas or overexposed areas, then HDR may not be needed. In that case, if you attempt to force the "HDR" look, the result may not be what you want.
Be sure to check the obvious: Did you use a tripod? Are the three images aligned? It seems to me that CS3 auto-alignment is better than the Photomatix (standalone version) alignment. But sometimes auto-alignment is a problem.