I thought I'd explained this, Jon. Let me have another go.
A normal "linked" image in a book is NOT a cover image - even if it appears on the first page of the book. A cover image is especially marked as such in the file. The "Cover Image" menu item in the Windows mobi reader will display it, and the library manager on the Gen3 will automatically display it as the book's "cover" in the library.
When you use "mobi2mobi" to add a cover image to a book, you are adding that special flag to the file which says "this image is a cover image". What the tool CAN'T do is go through the HTML code of your book and remove any OTHER references to that same image that it might find - and nor would you want it to, in many cases.
It's down to the book creator NOT to "link" the image that they want as a cover image within the normal HTML, but simply to add that image via the "Guide" section of the OPF.
With the older creation tools such as BD, there was no way to properly designate an image as being a cover image; all you could do with such tools was simply have an image link for the picture on the first page of the book. If you use "mobi2mobi" to "re-add" that same image as a cover image in such a book, you will end up with it duplicated - it'll be there once as a "real" cover image, and again as an image link within the HTML. In such a case, the correct solution would be to "explode" the book to its OEB source, edit the HTML to remove the image reference, then rebuild the book as a Mobi file with its "real" cover image.
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