Just wanted to say thanks for posting this, it solved my problem. I was having the same problem with Calibre when loading files on an SD memory card (SD card) in my PRS-505. At a certain point, I'd get directory errors when loading ebooks on my SD card, the same ebooks that would load on my ereader's internal memory.
I formatted the SD card as a FAT32 but then Calibre was not able to see it. After reformatting the SD card as FAT, I set Calibre to send all of its files and folders for the SD card to a directory named "books." This resolved the directory creation issue and allowed me to use Calibre to load ebooks on the SD card with no further problems.
Again, thanks for posting.
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