I have tried pressing the Reset button as soon as I click Upload, and also after the Upload is complete. There is no effect, still "L" remains lit indefinitely.
I do see that Reset is having some effect if I press it during the Erase procedure as it then says "SAM-BA operation failed" which is expected I guess.
One more thing, I noticed that just before the erase procedure my IDE says "Forcing reset using 1200bps open/close on port COM3". From reading the guide I would think this is only necessary for Native port programming and not when using the Programming Port as I am doing (but perhaps it is done for both?).
Dino