I’ve had numerous issues with HDR output from stitcher as well (even pre-Autodesk versions).. 

Have you tried just rendering out each “layer” then combining all the layers in photoshop or photomatix?

You’ll have to feed Stitcher each ‘source’ layer as well… meaning you can’t feed Stitcher bracketed photos.  For example, you’ll have to feed it you base exposure layer, then render out.  Swap out those photos for, say you under exposed, then render out...etc, etc… for each layer.

That make sense?

I have the exact same problem and did a search and came across this post. I am using 3 image for each position. normal 2 steps up and 2 steps down. I would really like to be able to output hdr then tonemap on photomatix. when i shoot inside and have a bright window i use dslr remote and bracket 7 images 2 steps apart sometimes i know that won’t work. i think somehow it cant handle the range. I saw in another post that ptgui is better for this.

I tend to batch convert all my bracets into individual EXRs using Photomatix, then load them as source images into Stitcher 2009. It’s really hard to see anything in the OGL view, but the stitch and render work well in any case. I also use “Morph” as my blending option as Smartblend on Mac has 32-bit issues…

Oh, I should also point out that using HDR images as input avoids the black artifacts…