OK, this one has me a bit confused.
I am building a "stand alone programmer" for ATMEGA328 chips, mainly to upload sketches, not the boot loader. I wired up a "basic breadboard Arduino" more-or-less following the example schematic of a DC Boarduino. Where I deviate is rather than using an oscillator, I am using a crystal and a couple of .1uF caps on pins 9 and 10 (of the ATMEGA328). The only I/O pins that I am wiring up are pins 2 and 3 for the serial data (again, the pin reference is to the chip, not an Arduino).
The problem that I have run into is this. I can place an ATMEGA328 onto my Boarduino, upload a sketch and have no problems. If I try to do it on my breadboard, the sketch will not upload unless I manually pull the reset pin to ground when I select "upload" in the IDE. With my Boarduino, I never have to touch the reset button.
My problem seems to be the reset circuit. From pin 1 of the ATMEGA328 I wired through a 10k resistor to +5V which holds that pin high. Between that I wired though a .1uF capacitor to the RST pin (6) of an FTDI cable. My "manual method" is a jumper between the 10k resistor and the ATMEGA328 pin 1 to ground.
My question is, what am I missing that makes me have to manually reset while uploading a sketch on the breadboard when I don't have to do that on a Boarduino?