I am having issues with uploading sketches to a bare SAM3X chip. I have my hardware configured like the USB programming port on the DUE, using an Atmega16u2 interface. I've programmed the 16u2 with the avrisp mkii programmer, with the firmware found here:https://github.com/arduino/Arduino/tree/master/hardware/arduino/firmwares/atmegaxxu2
(I've also programmed it with the .hex file read directly from the DUE 16u2 chip).
Using the same steps with a DUE, I am able to install the DUE programming port driver, and upload sketches in the Arduino IDE.
With my hardware, I am getting a code 43 (unknown USB device) when plugging into my PC. When I try to load the USB driver directly (from the arduino drivers folder), it doesn't install. I've read in a couple forum posts that the SAM3X is bootloaded by Atmel, and that there is no need to bootload the chip. Since I am observing this disparity between bare SAM3X and the DUE, I am unsure if the issue is in hardware or firmware.