I have had this problem for a while with the SD cards in both my PRS505 and PocketBook360.
I raised a ticket for it, #5625, a couple of months ago.
The SD card is detected fine by Windows and I can use the Save-to-Disk feature quite happily. The card just doesn't show up in Calibre's Library window.
It turned out that it was something to do with the card being detected too slowly by my PC. By the time it had connected calibre had already moved on. This was demonstrated by starting Calibre with either Reader already connected. Then the SD card appears in the library window with no problems.
I have to admit the SD card in my Sony is a bit rubbishy, I mainly use it for screencaps. The microSD card in my PB360 is a Kingston 1Gb, not exactly cutting edge but not that bad.
Kovid said (quite rightly) that he did not want to slow Calibre down for everyone else, so we left it at that.
I see that my ticket has been added to recently - in Russian - so when I can get a translation I will see if it's anything interesting.
...Ooh err...
wish I hadn't bothered it looks like some kind of porn has been added