I just posted and then erased a post saying it's impossible to have what people are seeing with pin 13. But then I got thinking that unlike older arduino boards the current rev3 boards (uno and mega for sure) use an opamp to drive the led, and if the bootloader puts pin 13 back to input mode before jumping to the users sketch (is that the case), then the opamp will be seeing a 'floating input condition', so maybe it's possible for the newer boards to have a 'interrmittent' pin 13 indication? Never occured to me as I don't own any Rev3 boards. Not sure how a LMV358 opamp might respond to a 'floating input pin' condition.
What do others think?
Lefty