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.