I have an arduino R2 smd.
When USB is plugged in, I can upload my sketch and everything work fine.
Now, when running on external power (12V on Vin), my sketch doesn't start until I press the reset button.
I read in the FAQ that the boot loader could see garbage on the serial port and loop, so I tried to pull RX (digital 0) down with a 10K resistor, but it made no difference.
EDIT: I just tried with another Arduino boat I bought at the same time, and this other one doesn't have that problem (also SMD R2).