Fastboot for win32 requires that you install and configure libusb-win32. Otherwise it will not see the kindle as a fastboot device.
The linux version of fastboot does not need special drivers, but you should set fastboot mode from diags, so that it gets saved. Otherwise you will have difficulty going from windows to run MfgTool, then switching to linux to run fastboot. If the USB port disconnects of reset, the kindle will drop out of fastboot mode.
It will be easier to use it from windows, but only after you have the libusb-win32 drivers working.