Originally Posted by taming
I am not sure if the flavor of Linux Kobo uses is compatible with FAT32. Maybe one of the Linux gurus here can tell us a bit about that.
Well given the internal memory and SD cards are formatted for FAT16/32 which the Kobo reads your ebooks from it most certainly is supported. I suspect the ROM?? in the Kobo used to perform the firmware update doesn't have FAT16/32 support compiled in to save on space, or maybe it is overlooked. Then again, as the internal memory is FAT and doing the update through the desktop app succeeds.....
I guess that end of the day Kobo didn't anticipate people wanting to perform the firmware update themselves via SD card (or needed to) and opted for a more user friendly approach and having it "automated" through the desktop app.