Uno bootloader issues with ft232 chips

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?

The optiboot bootloader uses a higher upload speed, which the FTDI chip may not be able to support. I'm not sure about this, though.

Thanks for the response, but the problem isn't with loading. The problem is simply getting the atmega328 to boot correctly. I've explained the electrical glich I was trying to debug here: FT232 dtr pin dropping low during powerup causing reset issues on atmega328 - Page 1

Once I figured out the older Arduino bootloader helped fix the issue then I thought this would be a better place to ask the question.

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.