The cover as a dot usually means a sideloaded kepub that doesn't have a cover defined. I think there was another cause, but I can't think of what it was.
How the covers are generated depends on the book type. For epubs, the device renders the first page of the book, and uses that as the cover. For sideloaded kepubs, it looks for a definition of the cover in the OPF file. The extended driver modifies this so that the cover will be defined properly.
There can be a problem for sideloaded kepubs if there isn't a cover image or if it is defined incorrectly. In this case, the extended driver can't add the property that is needed for the cover to be recognised. I have some books that have a text only cover, and this happens to them.
You should be able to fix this in calibre using the Polish books function. This will add the cover to the epub and do all the definitions. If there is already a cover, if it can be found it will replace it and fix the code. If it can't find the cover, it will add a new one at the start of the epub. That can mean you end up with two covers.
The upload cover options with the standard driver should work. This works by generating the cover image and copying it to the device. The only reason I can think of for it not working is when you start getting a lot of books on the device. Somewhere over 2000 books start having issues with the covers.
If a book is on the home screen, replacing a cover sometimes doesn't appear to work. The device seems to cache the covers and some other info for books on the home screen. They don't get updated until the book leaves the home screen or the device is restarted.
The upload cover options for the extended driver might not appear to work if, as I said above, the epub doesn't have the cover defined properly. In this case the devices database will not have an id for the cover images, so won't pick up the uploaded covers. The extended driver sets an image id in the database the next time the device is connected. After that, the cover should start working with the above issue about cached images and information.
If you still have a problem book, I would have to look at it. If it can be attached here, then do so. Otherwise, send me PM for an address to send it to.
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