There will be a post on the blog on friday about this

Was this posted to the Arduino Blog, or elsewhere? Didn't find any mention on the Arduino Blog, and looking forward to seeing this through.

try placing a diode between RESET and +5V on the POWER connector, with the cathode (end with the bar) towards the +5V.

Following up on my earlier "me too" post to this thread, can confirm that adding a 1N4148 between RESET and +5V has fixed the problem my Uno R2 board is experiencing also.

Thanks foubarre for the scope work, and robert rozee for your intuition.

We finally found that simply taking a 4.7k resistor from the board 5V to pin 7 causes the problem. On original UNO, this works.

Can you reproduce? (we can, each time, using any program, even 'blink')

Further to previous post, have replicated this simple test too - if digital pin 7 is high my Arduino Uno SMD R2 fails to run the bootloader led sequence (let alone run any sketch) after power cycling, until the reset button is pressed.

Any other Arduino Uno R2 owners able to replicate?

Can you reproduce? (we can, each time, using any program, even 'blink')

I can confirm this... just struggled with this for a few hours!

I have an Arduino Uno R2 with a WiFly shield (which connects Digital Pin 7 to an IRQ line on the SC16IS750 with a 1K to 3.3V; see http://www.sparkfun.com/datasheets/DevTools/Arduino/WiFly_Shield-v17.pdf).

Exactly the same behaviour as described.

Works fine after loading a sketch over USB, but after power cycling the Arduino halts -- that is, the bootloader led sequence does not occur and the sketch fails to run. Pressing reset results in the expected bootloader led sequence and the sketch then runs. Severing the connection between the shield and the D7 pin on the Arduino corrects the behaviour.