Thanks for the help so far. I will explain more about what I am doing, and the settings I have tried.
Firstly, I have tried the canvas settings, and this works for the built in viewer only.
To explain what I am doing, I need to get the captured image into a state that I can expand full screen without any title bars or menus. The only way I have found to do this is in a browser, eg Firefox, by using the F11 in FF to totally maximise an image. So after I capture the image in SC, I launch Firefox and pass the created file using "%file%". This works, but the created file (which is png), does not have the canvas settings. It has a permanent white background behind the shadow. The shadows don't seem to change with either the canvas settings or the settings in Special Effect Options. Eg, I can set the Backgnd to Red in Special Effect Options or in the Canvas settings, then capture an image and look at the autosaved png and the background is white.