I was able to do some testing and so far the solution to this elude me. I've attached a screen shot that shows what I'm getting so far. Any input is appreciated. To explain: column 1 represents raw panels #5 over #6. Column 2 is the STF version of each frame. The top STF'd frame, panel #5, is the HDRComposition frame. Panel #6 is just a regular stack (the level of noise in this unprocessed image is exaggerated in part by the aggressive STF, but it's still surprising as it consists of 21 total frames of 12x20 minutes and 9x15 minutes integrated with WSC...also of note is a problem on the top edge which is unfortunately a bright star just off camera which I thought I could deal with in post-processing somehow...later).
Column #3 is the result of performing StarAlignment | Register/Mosaic with Frame Adaptation and the final column is with STF applied. Already things do look right. Note that I did convert the HDR frame to 32f and the results at this stage of processing look the same. The merge mosaic processing resulted in a final image that looks nearly identical to the the one in column #3.
I also tried to add this problematic panel #6 to another part of the mosaic. In each case it exhibits this greyed out look to it. There is something wrong with this panel relative to the others....
In case you want to see the actual files a Skydrive link is included. I also included the combined panel a1-a4 to demonstrate that the processes in PI are working well as demonstrated by this very preliminary result (GMM has not been done on this part yet, but I know it's all good since I did it on just panels 2 and 4 which would be just B33 and adjacent areas).
Aquisition details on the panels: all acquired with FSQ106iii @ f/5, Mach1GTO, QSI593wsg, Astrodon 5nm HA, -15C and -25C depending on the weather with ~24 darks, ~12 flats, >50 bias. All panels at least 4x900 and 6x1200 (the target is to get to at least 16 total frames per panel to keep the exposures nearly the same and to have enough to combat noise). Panel 5 with M42 is 5x60, 5x300, 6x600, 6x1200.
http://sdrv.ms/Hp2L9cI would just choose another tool (PS CS6) to do this, but believe it or not I don't know how to do AP processing in PS as much as I do PI since I decided to start out with PI from day 1. I know enough about it to pull this off, but would rather get this tool to do what I know it should be able to do.
Thanks for looking.