I'm getting the exact same problem. I have created the epub file using Sigil bring this into Calibre and export to mobi.
The mobi file ilustrations appear to be all right in, Kindle, Mobipocket Reader and Calibre, all on the PC. However, on sending the files to an actual Kindle the top 10%, or so, of the illustration duplicates? But not ALL illustrations do this, some are all right??
The illustrations were taken from PDF using Acrobat to cut and paste the illustrations into Photoshop and exporting jpgs. I have tried reducing the illustrations to ridiculous proportions, almost postage stamp size.
I tried Mobipocket Reader to import the original epub files to create a mobi file but it doesn't import the file. I may be doing something wrong. But there aren't many alternative ways to import into Mobipocket Reader.
Any help would be most appreciated.