Hi Jose,
By "doesn't honor" what do you mean exactly:
- That the Bayer matrix that you select is not remembered by the script.
- That the deBayering process is not working correctly.
In the first case, it is very strange since the script saves the Bayer pattern as part of its settings, which are re-loaded each time the script is executed. I have checked this and it works correctly.
In the second case, a possible cause could be inconsistent FITS orientation settings. If you have the default FITS orientation (bottom->top) in FITS preferences, then when you use the script by default (top->bottom) the mirrored distribution of pixels will require a different Bayer pattern. Either change your default FITS preferences to set the top->bottom orientation (recommended), or change the orientation in the BatchPreprocessing script.