So, you're saying that when you ran the "Scan: local disks" task manually, it takes hours, and when you schedule it, it takes 20 minutes?
How about the number of scanned files in the final statistics?
I'd probably suggest to enable creation of the report file in the configuration of this task (or a copy) and compare them.
Generally, the only thing that could make a difference is the user account the scan is running under - when you run the task manually, the scan is run under the currently logged-on user, while the scheduled tasks are run within "avast! Antivirus" service, i.e. under LOCALSYSTEM account by default.