Originally Posted by kovidgoyal
Just a note: In the next release the default template will be changed to not put books into sub folders, as there are apparently devices made by some incompetent *cough*Amazon*cough* people that dont recognize files in sub-folders. So if you want to have books in sub-folders you will need to configure the device by right clicking on the device icon in the calibre toolbar when the device is connected.
This isn't just a Kindle Fire problem. We had to do the same thing in the wireless driver used by Calibre Companion because Kindle for Android does not support subfolders on any device.