Why don't you try burning the bootloader directly with avr dude commands on the console?
Sometimes the Arduino IDE just doesn't want to burn (happened to me more than once). Then I used avr dude commands on the console (cmd.exe for windows users) (you must install avr dude first) and then I could burn without trouble.
Edit: This is the command I use
avrdude -c usbtiny -p m328p -U flash:w:bootloader.hex
In your case you should change "usbtiny" for "arduino" because arduino is the programmer. Instead of "bootloader.hex" just write the bootloader you want to burn (look inside the Arduino folder instalation).