I'd say that you actually found your problem using sRGB with CR2's. Sounds like Photomatix is not handling the files correctly.
I did read this "photomatix uses a special approach........ ..... If you use Photoshop® CS2, you are left with a 16-bit image in which the distribution of tonal values still isn't quite right. You must tweak it using a curves adjustment."'
From
here.