[Charles Gantt] and a few others were having trouble burning the Sanguino bootloader to an ATmega644 chip. With some help from the [Nils Vogil] via the RepRap IRC [Charles] got it worked out and wrote a guide for burning the bootloader using an Arduino as an ISP programmer.
We’re not familiar with the specifics of the Sanguino bootloader, but [Charles] mentioned that he was unable to flash it onto the AVR chip without a resonator. The resonator serves as an external clock source for the chip. We’d bet the programming process changes the fuse settings on the chip to use an external source. Without that source, you won’t be able to communicate with the chip afterwards.
The solution just adds the resonator to the programming circuit. This should be useful when burning any bootloader using an Arduino. But it does make us wonder if there isn’t an alternative method that would let you draw the clock signal from the Arduino itself?