My Kindle and other usb-flash devices is mounted by udev rule which is calling mount with default options (no flush).
Flush option making most of old usb-flash drives is extermly slow, so I prefer faster defaults.
Kovid, if you can do something to fix Calibre with default mount, please please please do it.
Both os.fsync() make "Linux-vs-Kindle-problems".
I hope now you can repeat it on your system.