I have had the same problem where I converted a Text document to epub, added a cover via Calibre and then just got the generic Calibre cover. The cover I had downloaded came next, ie was page 1 of the document, but I can't get it to show as the cover.
I read in another thread (can't remember which one) that the next Calibre version would have something in it to fix problems with covers. From memory that was about a week ago, so maybe it is coming soon.
I have had a separate problem just in the last couple of days where I have epub books in the Calibre library and do the "send to device" one book at a time. It appears on the Calibre library and the device library that this has happened, but when I unplug the reader, only some of the books have gone across. For example, I just tried sending eight books, one at a time, ie not highlighting all eight at once. Three went across, five didn't.
However, I have got round this by opening the Calibre Library folder in Finder (we have a Mac) and then pulling across the books one at a time into the ereader showing on the desk top. That worked for me, so could be worth trying if others are having that problem. I assume that those with Windows could do something similar.
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