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Could you try flashing your Netduino Go with the attached (unofficial) firmware? Just flash all three files using ST's "DfuSe demonstrator" program.
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Doing this solved my problem:
Running the ShieldBase firmware update stalled at line 180 in STM32Bootloader.cs
_bootloaderPort.Write(true);And nothing happened until I forced the execution to stop.
I flashed the Netduino Go with the unoffical software and ran the ShieldBase firmware update again without any problems