Burn arduino bootloader using ubuntu 16
I had same problem and I think I have solved it.

In boards.txt file, I had:

##############################################################

diecimila.name=Arduino Duemilanove or Diecimila

diecimila.upload.tool=avrdude diecimila.upload.protocol=arduino

diecimila.bootloader.tool=avrdude diecimila.bootloader.low_fuses=0xFF
diecimila.bootloader.unlock_bits=0x3F
diecimila.bootloader.lock_bits=0x0F

diecimila.build.f_cpu=16000000L diecimila.build.board=AVR_DUEMILANOVE
diecimila.build.core=arduino diecimila.build.variant=standard

## Arduino Duemilanove or Diecimila w/ ATmega328
## --------------------------------------------- diecimila.menu.cpu.atmega328=ATmega328

diecimila.menu.cpu.atmega328.upload.maximum_size=30720
diecimila.menu.cpu.atmega328.upload.maximum_data_size=2048
diecimila.menu.cpu.atmega328.upload.speed=57600

diecimila.menu.cpu.atmega328.bootloader.high_fuses=0xDA
diecimila.menu.cpu.atmega328.bootloader.extended_fuses=0x05
 diecimila.menu.cpu.atmega328.bootloader.file=atmega/ATmegaBOOT_168_atmega328.hex

diecimila.menu.cpu.atmega328.build.mcu=atmega328p

## Arduino Duemilanove or Diecimila w/ ATmega168
## --------------------------------------------- diecimila.menu.cpu.atmega168=ATmega168

diecimila.menu.cpu.atmega168.upload.maximum_size=14336
diecimila.menu.cpu.atmega168.upload.maximum_data_size=1024
diecimila.menu.cpu.atmega168.upload.speed=19200

diecimila.menu.cpu.atmega168.bootloader.high_fuses=0xdd
diecimila.menu.cpu.atmega168.bootloader.extended_fuses=0x00
 diecimila.menu.cpu.atmega168.bootloader.file=atmega/ATmegaBOOT_168_diecimila.hex

diecimila.menu.cpu.atmega168.build.mcu=atmega168

##############################################################


I have replaced the line containing:

diecimila.menu.cpu.atmega328.bootloader.extended_fuses=0x05


with:

diecimila.menu.cpu.atmega328.bootloader.extended_fuses=0xFD


Everything is ok now.

I can install boot loader on an ATMEGA328P (with an usbasp programmer), and I can install sketchs after that (via usb serial).

I don't know if it's the best way to solve the problem, but it works.
Hope this will help you, if not already solved.