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I downloaded Flash.C to the Pro board. I needed to put a jumper between the
LoadC pins. I have to remove the jumper again to run the code.

When using an FTDI cable or SparkFun breakout board, this is needed, as the
documents state. Both of those only have one control output for RESET. To
force ISP mode you need to hold the loadC pin low which our USB dongle does.
MakeItC also prompts you for that if you tell it you are in Manual mode.