In Siril’s photometric color calibration panel the focal length of the telescope changes from what I set (660 mm) to a different value (653.9 mm). In fact, no matter what number I put in for the focal length it come back with 653.9 mm. I assume there must be a setting hidden somewhere which is overriding my input (which does not make sense). Any suggestion as to what I need to do to fix this?
This is both an input for the plate solve and the display of the result of the plate solve: 653.9 in your case would be the actual focal length of your optical system.
Yes, the initial value is used to compute the field of view that will be used to get the stars around the provided image centre coordinates from the catalogue to compare with those in the image.