@Lazar-Demin just tried flashing the dock and it worked for one of the docks
one of the docks continued to display the error.
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For the dock that did work:
I wired the dock as you suggested with 3.3v and GND wired to the dock.
Function SPI MISO -> Mini Dock and Omega Pin 1 -> Arduino Dock Pin 12
Function SPI SCK -> Mini Dock and Omega Pin 6 -> Arduino Dock Pin 13
Function SPI RESET -> Mini Dock and Omega Pin 7 -> Arduino Dock Pin Reset
Function SPI MOSI -> Mini Dock and Omega Pin 19 -> Arduino Dock Pin 11
Function VCC -> Mini Dock and Omega Pin 3.3V -> Arduino Dock Pin 3.3V
Function GND -> Mini Dock and Omega Pin GND -> Arduino Dock Pin GND
Here are some photos of the wiring.
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I then powered the minidock which and ran the script on the Omega via ssh terminal.
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So for me. One of the Arduino Docks works but but it looks like the other one does accept the bootloader (might be fried.)