I checked in the optimizer my new pano, and it says "very good" so how come when I stitch it together the picture turns out with muddy exposure. All the images were 3 bracketed F11 250 exposures and put together with Photomatix HDR.
The optimizer report of "very good" refers to the success it had in aligning the control points. It has no direct relevance to "muddy exposure". If the control points are well spread out over the full length of the overlap areas, then the general alignment of the images should be good. Sometimes, automatically generated control points are bunched together instead of being nicely spread out. This doesn't enable the lens distortion correction parameters to be evaluated very effectively, so while the images align well in the areas where there are control points, they might well not align in areas where there are no control points (typically in the corners of the images). The solution is to add extra control points manually to improve the spread. What all this might have to do with "muddy exposure" I don't know. Are the images being merged with Photomatix before stitching or are you merging the output stitched equirectangular images?
Are you using PTGUI to stitch your panoramas before loading them into Photomatix? If so, make sure the stitching parameters for all three of your bracketed panos are EXACTLY the same before before loading them into Photomatix. Fully automatic stitching in PTGUI will lead to slight differences in your three panos, which is enough to create a blurry muddy look when loaded into Photomatix. Also, selecting the "align source images" box in Photomatix will ensure perfect alignment.