Markus_L811:
Did you install the inf for the nativ Usb-Port and try to program it from this one too?
There is no change in Device Manager when I connect to the Native USB port (as there was when I installed the drivers on the Programming port), so I am not sure how to install the driver?
Palliser:
I recommend to try with another machine and IDE (may be W7 and IDE 1.5).
I just tried it in Ubuntu 12.10 as a virtual OS on my Win8 machine, and I get the same result. Compiles OK, and the IDE tells me the Upload went OK, but no change on the board. Will see if I can get hold of a real Win7 machine later today.
I am going to post this problem over on the Adafruit forums to see if I can widen the exposure of my problem.