I've just come across this problem where my scheduled tasks were failing due to this setting violation following an upgrade to QVS12. I struggled for a while, contact support and we worked out what I was doing wrong. Solution below:
1. I'd already tried the suggested solution to add AllowExecuteCommand=1 to Settings.ini. Stopped qlikview services, restarted services after saving the change. Didn't work.
2. Turns out i was updating the wrong Settings.ini file. I was updating the one in the QllikView Server folder. The one you need to update is here C:\Windows\System32\config\systemprofile\AppData\Roaming\QlikTech\QlikViewBatch
Update the Settings.ini file here, setting AllowExecuteCommand=1 stop services, save changes, restart services.