Hi Steve,
Neither will it debayer the original fits files.
FITS files cannot store information about CFA patterns in a standardized way. I see a 'DEBAYER' keyword in the screenshot you've posted, but this is a nonstandard keyword invented and used internally by a particular application. Our policy is to avoid relying on nonstandard metadata items generated by other applications.
So this is normal behavior. You have to select the appropriate Bayer pattern to debayer your FITS files, both in the BPP script and on the Debayer tool.
I register these images with the star alignment process, which converts them to .xisf files
As already noted on this thread, this is incorrect. Demosaicing can only be performed on calibrated raw frames.