To resolve this issue, open your master PDF in Ilustrator or Indesign. Expand the media box to the bleed area and save. Export this file to a PDF and reupload into eDoc as your master PDF. This should resolve the issue. Note that you cannot set the media box within Acrobat. Also, please remember that you should not have a bleed set in your master PDF. You will want to create the master PDF to be the size of the finished product plus the bleed. Then set the bleed inside of eDoc on the Template Info tab of the template.