If I remember correctly, the Photomatix watermark appears in the bottom corner right? If it does, just take the picture before you do HDR, and make it 50 or so pixels taller, then put the picture at the top and leave a white gap at the bottom. The watermark then goes onto the white gap, then just crop your picture back.
I can't remember if thats Photomatix or not though. Tell me if that works, if not i've got a couple of ideas.
actually.. yeah, one question. After I convert the files into an HDR in photoshop and save it as a .hdr file and open it in photomatix, the shadows are coloured like, blue... or purple.. why? And even after I've processed the hdr in photomatix, a small amount of the colour in the shadow shows.