NB,
I had this problem for over a year, & I finally cracked it with the help of Toad support along with trial & error. Make sure that your scheduled tasks that are created from the Toad Automation are configured as "Windows Server 2012 R2". Also, make sure to select the checkbox "Run with highest privileges". These settings are found at the bottom of the Task Scheduler Library in Server 2012 under each task. Be sure the radio button for "Run whether user is logged on or not" is selected but that should be default.
Please note, every time I create a new Toad Project & Automate, it creates a new schedule task configured as Windows Server 2008 by default without the highest privilege. I have to explicitly change these 2 default settings on new projects.
Hope this helps.
Eric