There are a couple of "flavors" for the Atmega328. The one that comes with the Uno R3 is the Atmega328P-PU which means this chip passed the low current operational testing at Atmel (Pico Power). If it does not pass this test it does not receive it's "P" badge and is just a Atmega328-PU. The problem is, it also receives a different chip ID and that causes the programmers to not program the chip. If you put an entry into the boards.txt file for the Atmega328-PU then it should bootload.