Craig,
Those are nasty dust motes. The CaLIGHTs masters are 32 bit floating point RAW fits files. Your DS10C generates 16 bit RAW fits files and, while I have never used "Fiji", I suspect it is expecting any fits file to also be a 16bit RAW format. It's easy to have CaLIGHTs convert any of it's master files into 16bit RAW fits.
Using the main CaLIGHTs screen click the "Select LIGHTs" button and load your master file. Now click the "Preferences" button and select a 'Custom" Pedestal Priority. Set the Pedestal value to 0 and then click "Save Defaults". You also need to ensure that the Multiplier is set to 1 and that no filtering is selected (Noise filter, Bad Pixel Filter, Row Noise Filter, etc). Don't have any files selected as Master FLAT, Master DARK, Master BIAS etc. This will ensure that CaLIGHTs will strictly convert the floating point values to 16 bit integers. You will notice that the 'Calibrate" button is no longer disabled and grey. Click the "Calibrate" button and CaLIGHTs will create a
calibrated 16bit RAW version of your master file. Just remember the calibrated file will be saved to a subfolder. [There is a text statement in the Calibration Progress Report that starts with "All files will be saved to..."] I went ahead and used the procedure to generate a 16b RAW version of your master FLAT and saved it to your google drive folder.
Good Luck
Peter