Leon,
All I can tell you is to make sure that the logo is of the proper size. We have seen where the improper size causes it to not be printed. From the user guide:
"Best practices is to use a logo or banner image that is 600 x 100 pixels (width x height). The WebUI does not apply the size restrictions when you upload an image file, but the image is resized to 600 x 100 pixels when it displays or is printed."
If that does not work, please open a TAC case.