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@Draccy: That almost certainly because those files have some formatting that adobe digital editions (the software used to render the files on the reader) doesn't support.
I try to work around as many limitation of ADE as possible, but there's no way to get 'em all. I suggest opening a ticket on te calibre website and attach one of these files that when converted dont display in ADE. I'll see if I can find a workaround for whatever the problem is.
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