Due circuit minus the slow programming port (Native only).
The new boards are recognised until I program them, windows then sees nothing attached at all! I don't even get the windows beep when I plug it in, but hit erase and sure enough windows beeps and it shows up.
What sketch did you program them with? I mean, this sounds like "expected behavior" for the native USB port, UNLESS your sketch explicitly includes USB code. No USB Code, no USB activity. The autoreset/upload features of the arduino are implemented either by having the 16u2 fiddle with the reset and erase signals, or by having the usb code from the previous sketch recognize the "reset" command... (I think.)