Thanks, that's a good idea to use Photomatrix's other tone mapper.

I took 3 shots in each "bracket". I shot in A-priority, therefore all shots had simialr exposure/brightness even though the sun was setting.
I seperated the 3 sets of files on my computer (light, normal, and dark). I used LR-Timelapse to "fade" the images over time, so they looked reasonable for a sunset.
I then put the 3 sets of images into the same directory and ran Photomatrix. the resulting images no longer faded over time - it seems Photomatrix must have performed an "auto brightness" function. I need to force myself to work on it some more (and perform the suggestion here of using jpegs, but I thought an earlier direction said it does not work on jepgs).