Sounds like your images may not all be of the same size (number of pixels in X and Y). Perhaps you cropped some and not others? Or maybe some are debayered and others not? Or maybe different debayering was used on different images?
One way to check image size (probably there's an easier one) is, under Image>new click "set as active image" and the pixel dimensions will appear.
Are all the images color? I don't think PI takes kindly to darks/flats that are grayscale operating on images that are color.
Hope that helps.
Alex