I'm working on custom pcb that uses the Arduino bootloader. My hardware uses an ft232 chip to allow programming over usb like the Arduino Duemilanove used. I thought I'd just use the newer Uno bootloader and it worked fine on 75% of my boards. 25% showed issues where I would have to power cycle the chip a few times to get it to boot correctly. I was quite confused, but eventually figured out if I when to the Arduino Duemilanove W/ ATmega328 the problem goes away (more testing on additional failing chips need to verify this always fixes the problem, but I think it does). I know the Duemilanove used the ft232 chip like I use and the Uno uses some other atmel chip.
Does anyone know why the Uno bootloader might not work reliably with the ft232?
I use a 100nF ceramic capacitor for auto-reset on all my boards. Works every time. The trace of the reset pulse looks very strange. It should be at 5V most of the time (pull-up), dip down to 0V then go up to 10V and back to 5V.