The issue ended up being a new feature of the windows 10 console. Under the default config, whenever you click on a command window in windows 10, it immediately halts the application process when it attempts to write to the console. When this happens, the command window has gone into "selection" mode.
You can tell it has happened because it will prefix the title bar of the command window with the word "Select" :
To get your program running again, you have to press escape or click somewhere else.
To get rid of this strange behavior, you can disable QuickEdit mode:
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