Hi Larry,
Ok, for clarity, just in case we are talking about a different workflow. What you should be doing is along the lines of:
Pre-process as you have been, but don’t integrate, or if you are, don’t use those files. Do this separately for each night’s images, assuming you took separate flats for each night/filter.
Open StarAlignment.
Ignoring any registered images produced by the BatchPreprocess, select a calibrated image to align to (the reference image). By calibrated I mean, it has had the appropriate flat, bias & dark frames applied. The important bit now is this should not be changed to any other image during the whole processing of this object, even months in the future should you want to add more data. A luminance reference may be a better reference image if you took any.
Click on Add Files to add all the subs from all the 3 nights in one go. This may mean pressing the Add Files button 3 times if your red filtered subs are located in different folders.
Set an output folder
Execute StarAlignment
Now repeat the above process for the green & blue subs, but keeping the same red reference image.
Once all the 3 filtered subs from the 3 nights are registered, then run ImageIntegration to combine all the red subs from all three nights in one operation, repeat for the green & blue.
For more info on the settings for integration see:
http://pixinsight.com/tutorials/master-frames/en.htmlAlternatively to the above workflow, so long as you select the same reference image when using the BatchPreprocess for each of the filtered subs it should work. Doing it this way means you can now just integrate the registered files created by the script, a bit quicker and easier.
The problem you may be having is not using the same reference image for all the images or I have completely missunderstood the problem.
I hope that helps,
Mike