Is there a specific reason for running the WinDU tasks on a schedule?
What are the specific task you have in mind?
I would think you could make a report similar to check what needs to be checked. (Using Info*Engine/Webjects/ect.)
If you are on a unix system you could write a cron job to run windu.sh, but that would just open the utility, you would need to find a way to send params and run the utility. I am not sure there is such a way.