This is probably a FITS orientation issue. If you haven't changed it, the default FITS orientation is bottom-up in PixInsight: The origin of coordinates is at the bottom left corner of the image, X coordinates grow from left to right, and Y coordinates grow from bottom to top. This is the standard orientation used for FITS images generated with professional equipment and acquisition software.
Unfortunately, most amateur image acquisition software generates FITS images with the up-bottom orientation: Origin at the top left corner, X grows from left to right and Y grows from top to bottom. If the orientation that you have selected for FITS images is not up-bottom, then your CFA raw frames won't be deBayered correctly.
To select the up-bottom FITS orientation:
1. Open the Format Explorer window.
2. Double click the FITS item on the left panel.
3. On the FITS Format Preferences dialog, Miscellaneous Options section, select Coordinate origin = Upper left corner.
4. Click OK.
Now open one of your raw frames and find the correct Bayer pattern to deBayer it. This is the same pattern that you should select in the BatchPreprocessing script. Note that the BatchPreprocessing script automatically forces the up-bottom FITS orientation by default (irrespective of the global FITS Preferences).
Let me know if it works as expected this time. The FITS support module included in the incoming version 1.8 of PixInsight uses the up-bottom orientation by default. Hopefully this will prevent these problems in the future (but then all professionals will complain, of course...).
Rob: Actually, I am working on PI 1.8 full time during my (supposed) vacation time. We *really* need a 1.8 release in September, so no vacation this year.
