If there aren't too many images, you can use the "Tweak Epub" option to explode the epub, open each image in your favorite image editor (if you don't have one, Paint.NET works well on Windows), re-invert the image to get it back to normal, save, and then pack the epub back up. I've had to do that several times with PDF to Epub conversions. It's tedious, but if everything else is good and the number of images you have to edit is small then it's the simplest fix.
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