Here my 2 cents worth on photomatix. Noise after generating HDR is due to a lot of reasons.
it depend a lot on:
the iso setting (I usually use iso100 - 200) when taking the 3 exposure.
When processing HDR. remember to check the "reduce noise" box
the setting of the tone mapping in photomatix.
in the detail enhancer column, do not be too aggresive on the strength control. setting to 100 will create a lot of noise... keep to 60-75.
Smoothing section also keep to mid to max. Otherwise halo effect will also create a lot no noise.
In Misc Settings, Boost the Micro-smoothing to help reduce noise.
Last but not least, need to use photoshop to touch up a bit on noise reduction.