I think the first one is the easy one to explain. What options do you have set on the update metadata dialog? The firmware doesn't read the publisher, published date or ISBN from sideloaded books. If you have these selected, there could be a lot of books to be updated. Plus there are any other changes to the books metadata that gets updated.
For the rest, do you use a plugboard to put the series info in the title? There was a bug in matching books between the device and calibre library if plugboards were used and there was a book on the device whose filename didn't match the plugboard. In this case, the series was set to the first letter of the filename. I thought I had fixed this, but maybe it has come up again. I'll have a look.
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