This "Only allow one instance of the protected workbook" option stops end users from running another instance of the protected workbook if one is already opened. If the end user tries to run the EXE again, the initial instance gets focused in the task bar. This inhibits end users from opening several instances of the same protected workbook simultaneously.

 

 

On Excel versions lower than 2013, a message box with “An instance of this application is already running” will be shown instead of the window being focused.