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Jack,
I can only repeat what I said earlier. I have had no issues since I have been making conversions prior to downloading. There is a post under the calibre forum that goes into detail about the problem and its related to how the cover was attached or packaged in the epub.
It appears you and I are having different experiences with calibre. I don't doubt you are having issues and they may be related your specific mix of hardware, operating system, calibre version. I hope you will be able to work it out soon.
Harley,
I think the issue with covers, at least the issue I had with covers, in most cases will be fixed by doing a conversion from whatever you have to whatever you want. I don't think it matters much whether it is from lrf to epub, mobi to epub, epub to epub etc., As far as formatting issues (does it mess up anything else) I rarely reformat a PDF because I don't normally care for the results.
However, there is a new version of calibre 0.8.11 which preserves the original format when doing a conversion. I don't have any experience with it yet but if true, you should be able to reformat without risk. If you don't like the result you still have the original pdf version.
But check this all out by reading the change log at calibre's site. I did a quick review when I upgraded the new version today but I wasn't paying close attention.
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