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Roger,
Photomatix will handle small misalignment errors. As always, when bracketing, and wherever possible, you're better off using a tripod.
If you have any wind at all and are photographing anything with foliage, the movement between frames becomes quite apparent as a sludge and blur in the final Photomatix'ed output.
However, for optimal results, you're better off exposure bracketing and combining with layer masks afterwards. Photomatix does strange things when it comes to sharply defined objects/lines, such as power lines or fences. It seems the algorithm doesn't work nicely around those types of objects and you end up with interesting artifacts including halos around those particular objects.
This doesn't even begin to address issues regarding saturation and contrast, and, the algorithm illuminating a pixel with what it thinks should be there, rather than what should actually be there.
My $0.02, including GST. Your mileage may vary.
H
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