I have two arduinos, one Uno and one made by myself using Atmega8 and http://itp.nyu.edu/physcomp/Tutorials/ArduinoBreadboard scheme.
I turn Uno to ISP programmer using proper sketch and disabling auto reset using a cap between reset and gnd pins. And problems begins... I burn bootloader on second board without problems, next I used blink to see some effects :) After that I use sketch that give HIGH to all digital ports (to test solders and connections)... but all circuit is dead. I burn bootloader once more, use Blink and it works... till next upload.. It seems that cotroller wipe bootloader from memory. Some advices ?