(HELP) AVR Serial Port does not work.


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Please help.

I have a Papilio Duo 512K and I am running Windows 10. I can't upload a sketch from the DesignLab IDE without the use of an ISP bit file. I need the FPGA for other needs, so I cannot program using ISP.
I have read through and found that programming directly over USB is possible: http://learn.gadgetfactory.net/2015/01/15/designlab-quickstart-duo-avr/ 
However, this did not follow my expectations and the device is nowhere to be found. Every time I press the FPGA reset button, the Papilio DUO AVR Serial Port becomes available in device manager and DesignLab. The moment I upload or lift my finger off the reset button, the serial port vanishes into the hidden devices.
Things I have attempted:
Uploading while pressing reset.
Burning the bootloader, but same issue as the AVR serial port.
Multiple uninstalls and reinstalls of the DesignLab IDE (Version 1.0.8) and included drivers.
FTDI driver installation.
Unchecking Serial Enumeration.
Direct connections to PC, No USB hubs.
Please help me fix this issue.
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Figured out how this works with some help.

I flashed the .bit file of my design to the internal ROM using Papilio Loader (SPI Flash), then used the FPGA to flash the microcontroller using ISP. After unplugging and replugging, both keep their memory and work with their respective designs.

If you're using Xilinx ISE, set Arduino_Reset pin (P139) to high / '1' at the top level.

If anyone is using avrdude,

avrdude -p atmega32u4 -cstk500v1 -PCOM5 -b57600 -U flash:w:example.hex

Make sure to directly load the FPGA with a Papilio_DUO_ArduinoISP.bit file, then flash the microcontroller. It won't overwrite the SPI Flash where the necessary .bit file is located and the Atmel chip has it's own separate memory as well. This AVR programmer will vanish after a power cycle.

I hope this information can be helpful.

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As for the AVR Serial Port, it still doesn't work. It's not used for separately programming the Papilio Duo's AVR chip as shown in the videos and learning material. It irks me that the official information is false and led me on a wild goose chase. I hope someone can shed some light as to why my Papilio DUO cannot program from the AVR serial port or the bootloader.

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