We've created this Forum Thread with some workarounds and advice to assist you in publishing you ebook.
advanced one piece cover transparencies detected
I was using the one piece cover option and uploaded my 300dpi png file. After it uploaded the program alerted me that it found 'transparencies' in the file and corrected them (or corrected for them). When I looked at the pdf file the program generated, the picture had thin, grid-like lines affixed to it that were not part of my file, basically ruining the cover.
I tried merging all my layers down in GIMP and reuploading the png. Same thing happened. Should I save to jpg or some other format? I know png will preserve an alpha channel but I don't think I had any alpha channels going in the file in which I merged all my layers.