Originally Posted by ldolse
What happens is that Calibre sends the epub along with the configured thumbnail, but when the Sony sees a new book it extracts the original/ugly cover. Enabling automatic metadata management will cause Calibre to overwrite the cover on the next connect. Since it's no longer a 'new' book the Sony will stop overwriting it.
- ldolse makes a good point but if you want this to work automatically I believe you have to check some boxes in Sony's Device interface plugin (see attached).