Hi Brent,
PixInsight 1.8.5 implements a new automatic CFA pattern detection mode in the Debayer tool and the BatchPreprocessing script (which uses Debayer internally). This mode works perfectly for DSLR raw files. However, FITS files cannot store information on CFA patterns, so you have to select the Bayer pattern of your camera manually in the BPP script. The same is true for the Debayer tool if you use it directly.