foubarre:
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.