I restarted Calibre, deleted everything off the SD card and the device, and then transferred the books back to the card only, and this time it worked for some reason. I didn't change any settings so have no idea why now it's working..
But now one difference I noticed though with reloading all books is that the series info in the library listing doesn't appear like it did. Actually I don't think it appeared for every series, but it did for some, and now it's not there for any series. Did I mess up some other setting doing this?
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