We've created this Forum Thread with some workarounds and advice to assist you in publishing you ebook.
Background color missing in cover photo
I created a three-layer cover for a book. The lowest layer was the cover color and the next layer up was a photograph and text. The photograph had been converted into a shape in Photoshop by outlining it with the lasso tool and then creating a new layer via cut. Thus, all that was left was the image without the background.
The image, btw, was of a cat and the title of the book wrapped along the spine of the cat. All looked fine in InDesign and the subsequent PDF, but when the book arrived, the graphic box that was the cat had a white background rather than the color on the rest of the cover. Here's the PDF I uploaded. Thank you.