I'm surprised that -F works, but it seems to verify and progress is progress
The issue with the boot loader is that path
you cant use a : in the path without quotes, it confused avrdude
Try
C:\Program Files\arduino-1.6.9\hardware\tools\avr\bin>avrdude -B 8 -C"C:\Program
Files\arduino-1.6.9\hardware\tools\avr/etc/avrdude.conf" -v -patmega1284p -cstk
500v1 -PCOM5 -b19200 -e -Uflash:w:"C:\ATmegaBOOT_1284P.hex"
The issue with the boot loader is that path
you cant use a : in the path without quotes, it confused avrdude
Try
C:\Program Files\arduino-1.6.9\hardware\tools\avr\bin>avrdude -B 8 -C"C:\Program
Files\arduino-1.6.9\hardware\tools\avr/etc/avrdude.conf" -v -patmega1284p -cstk
500v1 -PCOM5 -b19200 -e -Uflash:w:"C:\ATmegaBOOT_1284P.hex"