What is the chip number you are trying to load a bootloader on? The Arduino uses a 328P and it sounds like you may have gotted a 328. A minor problem, and easy to work around, just means there are a couple relatively easy things to learn to get the bootloader working. Once it has the bootloader its just an Arduino chip.
If you want to learn how to use AVRDude directly I can give you the commands to program the chip - from a DOS prompt.