Hi Scott,
You're right to pick up on this but it's a bit difficult to know what to do about it as different processing programs have different ideas about how Bayer patterns apply in FITS files. For instance I can load the same FITS into PixInsight and AstroArt and in PI I need to use RGGB and in AstroArt GBRG
The cause of this is that FITS files are supposed to start at the bottom left (most images start top left). If this is followed then the bayer pattern for a FITS files (which describe the top two rows) should be swapped round in a FITS file compared to an SER file. This is what SharpCap does and it seems to be compatible with AstroArt and PIPP, but it disagrees with the way PixInsight expects the bayer pattern to be.
As you can see, this isn't something that I can fix 100% as if I swapped the pattern I wrote to the FITS file to make it what PixInsight expects then it would be wrong for AstroArt and PIPP. Maybe the best I can do is add a comment to the FITS header saying that the opposite pattern might be needed in some software?
cheers,
Robin