Ok so after importing one of my photos into AstroImageJ (I use this for producing transit plots) and checking the fits header, the image dimensions itself are 1677 pixels x 1264 pixels.
This is probably what is causing the errors in plate scale because I am saying the image dimensions are 3354 pixels x 2529 pixels. But how is this possible when the Atik 383L has a sensor size of 3354 pixels x 2529 pixels? I thought I had to put in the default size of the sensor as specified by the manufacturer.