I shoot RAW files - On this shot i have a JPG also - Problem - I was trying to save as applying a crop - I could not get it to save the new file with the crop. Finally I seperated the RAW & JPG - the crop was on the JPG not the raw and my setting was to use the RAW file. Very annoying & time consuming but I figured it out. Is it possible to have the crop on both? I'm not sure if they were seperate when the crop was added (Not usual).
Just something you might want to look at.