Sorry to hear about your problems kirk, Since I use mac systems I am afraid I can not help at all with the corrupted preferences issue. Regarding the various stitching software, I am working with CS3, APP pro and PTgui. I am shooting with a Cambo Ultima view camera with a Canon 1ds mkII mounted on the rear as a capture device, for lenses I use the schneider digitar 28 and various hasselblad glass. I like this set up for architecture as it allows me to create 9 frame stitches (there up and three across ) So far so good. Everyone is happy (including my accountant) but I am spending too much time behind the computer. My problem is that when I bracket my exposures (2 stops either way) and create the stitches the resulting files do not align precisely. They can vary from dead on to three or four pixels off, this is a pain because I like to paint (with layer masks) from one exposure on to another. Is anyone else have this problem ? The folks at APP suggested that in application settings I "Change "Detect links in" to "one stack level". This means there will be only one level of the bracket that has links and not all layers. Effectively, it will give what you want : every layer will have the same links" well that does not seem to be doing the trick.....
I can't comment on doing this in APP, since my past experience is that it didn't handle this scenario very well. PTGui can do it just fine, though. Just configure it to enable HDR stitching and link the layers. I prefer the Exposure Fusion option to the regular HDR processing. Then on the output tab, tell it to output the 'blend planes' in addition to the final blended shot, and it will give you what you want.
One word of warning, if you use Smartblend for the blending, sometimes it will blend slightly differently for each bracket and you'll get small alignment problems in certain parts of the image. I prefer to use the 'PTGui' option for blending when dealing with brackets.
