If you want to flash a ATMEGA328-PU (non pico power) with the arduino bootloader you have to change the chip signature.

I have created a "new" Board in Arduino which is only for flashing the bootloader.
Open [arduino-dir]hardwaretoolsavretcavrdude.conf in Editor and search for ATMEGA238P

youll find this line:

#------------------------------------------------------------

# ATmega328P

#------------------------------------------------------------

then copy the header with all information (to the next header) and paste it right before the next header.
Then change the Header, id, desc...

#------------------------------------------------------------

# ATmega328

#------------------------------------------------------------

part

id = "m328";

desc = "ATMEGA328";

...and the signature:

signature = 0x1e 0x95 0x14;

Save it and close avrdude.conf

Next Step is [arduino-dir]hardwarearduinoboards.txt:

You can copy and paste following lines:

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

unoFlash.name=Arduino Uno BL flash to ATMEGA328

unoFlash.upload.protocol=arduino

unoFlash.upload.maximum_size=32256

unoFlash.upload.speed=115200

unoFlash.bootloader.low_fuses=0xff

unoFlash.bootloader.high_fuses=0xde

unoFlash.bootloader.extended_fuses=0x05

unoFlash.bootloader.path=optiboot

unoFlash.bootloader.file=optiboot_atmega328.hex

unoFlash.bootloader.unlock_bits=0x3F

unoFlash.bootloader.lock_bits=0x0F

unoFlash.build.mcu=atmega328

unoFlash.build.f_cpu=16000000L

unoFlash.build.core=arduino

unoFlash.build.variant=standard

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

Please Note: This is only for flashing the bootloader! For uploading the sketch to the ATmega you need to select "Arduino Uno" or youll get an error.

If you use the AVR ISP MKII by Atmel youll need the driver which is located here:
[arduino-dir]hardwaretoolsavrutilslibusbbinavrisp2.inf