I believe I had used whatever the default is, which was Fat32 I think; I don't have it with me unfortunately. When you say that the laptop and Calibre see the card just fine, is it plugged into the Kobo at the time? Also, when you first added the content and disconnected, did you get the processing data message?
Another thing you can try; with the kobo on, pop out and then re-insert the memory card; does the kobo do anything? And before anyone says anything, this should not harm the card or the content in the least as it's not writing to the card; it's only reading. But of course, it's always prudent to back up your data, just in case
but I would still suggest that you try with epubs; I'll try PDF's and a CBZ file when I Get home as I've only really loaded stuff onto internal memory to date.