I have another problem. Sometimes, when I process true-colour source images under ST, the output margins become cyan instead of white (I have double-checked that the white margins option is applied to all pages). Here is an example image. I get a cyan line at the top margin. Maybe you can't reproduce with just one page only. Sorry for the filesize. It's 2.5MB
PS: I think that rather than the margins themselves it's the underlying canvas differences after deskewing. I am not sure though.