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The performance timewyrm seems to be talking about is getting to the shelf list. That shouldn't be looking at the books at all and only reading the database. How long that takes to display seems to depend on the number of shelves and the number of books on them.
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Unless some bright young programmer maybe decided to generate the thumbnails for each shelf before displaying the list of shelves? I bet that'd slow things up a bit... Perhaps it's just an issue with that many files in several shelves being checked or verified?
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The calibre driver doesn't copy covers to the device if the books are on the SD card. The recent firmware doesn't store the cover images or read them.
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Are you sure? I haven't tested, but could have sworn I saw that suggested if you checked the appropriate options in the Kobo driver in Calibre. (Doesn't make it so, of course.) I know the recent firmware doesn't store them, I didn't know it wouldn't use them if they were there... I suppose it wouldn't make much sense to copy them there if the firmware ignores their presence.