Sometimes, the PDF will need to be flattened so as to preserve the color when being converted to a digital edition.
To correct the color issue, the file needs to be saved as a postscript file, and converted back to a PDF before uploading so the colors within the digital edition stay crisp and match the transparency of the PDF. To save the file as a postscript, simply save the pdf as a .ps (postscript) then convert it back to a PDF, then upload into the admin portal.