Have you done ANYTHING to the .CR2 image before the SplitCFA? If so, maybe you altered its dimensions. Open the image in PI and zoom way-way in, center the cursor on the pixel in the lower-right corner--the pixel values (x and y), read by the cursor and rounded up, should be even numbers. If they are not, than the image has been altered or incorrectly transferred from the camera to the computer file. (You can use STF to better view the individual pixels (all of which should be gray...not colored).)
Alex