I think it's just a case of upgrading Photomatix (not matrix
)
Raw files from each camera are different (even if they have the same file extension) so it takes a little while for newer camera files to work properly in third party software.
Long winded solution would be to open the raw file in your raw processor (Adobe Camera Raw maybe?) and set the varying exposure levels, save each exposure as Tiff, and then load the tiffs into Photomatix and tonemap that way, it usually gives better results too. I find that it's more like working with properly bracketed images rather than letting Photomatix decompose the Raw file itself.