FileMaker Server 17.0.1 and 17.0.2
Windows 10 and Windows Server 2016
If the server is not setup for the current user to auto-login via external authentication and you run:
fmsadmin list files
You will be asked for username and password. If you abort via Ctrl+C, then run the same command again, you cannot type anything into the console when asked for your username.
Pass the command through cmd first, like:
cmd /c 'fmsadmin list files'
This can easily get complicated if you need to escape quotes in parameters, but this format appears to work:
cmd /c '"C:\Program Files\FileMaker\FileMaker Server\Database Server\fmsadmin.exe" close "My File" -y'
Some of the other options mentioned here might work, but I didn't have much luck with them: https://social.technet.microsoft.com/wiki/contents/articles/7703.powershell-running-executables.aspx