!"C:\Program Files\MATLAB\R2016b\bin\matlab.exe" -r NewFunction.m &
This tells the new MATLAB instance to run NewFunction using CLI.
However, it seems that it is trying to run NewFunction.m before MATLAB fully starts up and says, "Undefined variable "NewFunction" or class "NewFunction.m"".
Is there a way I can tell MATLAB to wait before executing the command? As far as I know this functionality doesn't exist in Unix/CLI.