Can't run drush from within website folder configured with IIS on Windows Server 2012
Drush Launcher solved the issue for me.

Step 1 Download drush.phar and put it in project root folder

Step 2 Create drush.bat file in project root folder and put following content (it will run phar in window)

@echo off
php "%~dp0\drush.phar" %*


Now it will use local drush.