No, unfortunately this is a bug in the final release of 2.1.2.
They switched the device drive names, so external card gets a higher priority than the device itself (you can see it in explorer, SD card is e.g. E: and PB602 is F

So Calibre thinks SD card is device and searches for a folder "books" which is normally not there and so finds nothing, while all stuff on the reader itself is shown.
They fixed this in final release
2.1.2 with fast update
.