AFAIK, this is an issue with the program ran by Task Scheduler, not Task Scheduler itself. Sometimes, you can create a batch file and start the program executable. For example, if you have created a batch file with the name avscan.bat in C:\, start it via Task Scheduler using the following command:
This line starts an instance of cmd interpreter, that reads the c:\avscan.bat file and tries to start it minimized. Also it wraps an exit command so cmd interpreter is closed after the batch file finishes.
cmd.exe /c start /min c:\avscan.bat ^& exit
Also, what AV solution are you using? Usually, some AVs already have a scheduler to start a silent scan.