the libRaw guys/gals started removing a row of pixels from the image at some point. that flips the bayer matrix, so it is no longer RGGB but GBRG.
in the linked thread juan says they had a good reason for doing this - i dont know what it is but i guess since most people expect libRaw to debayer the images for them, it is not something that they are going to notice (in other words, libRaw knows that it removed the row and changes how it debayers accordingly.)
the real problem comes if you have calibration masters produced with the old libRaw or DCRAW and you try to use them against lights made with the new libRaw. either that fails outright because the images are different sizes, or the calibration is outright wrong as the pixels no longer correspond to one another in the lights and calibration frames.
anyway if you prepare your masters and lights with the new libRaw then everything will work out, but you have to know that the bayer matrix is no longer what canon says it is. based on what mark has said it sounds like if you use Auto it should all work out OK.
rob
