Software Update ignores Scheduled Check under Snow Leopard

I've tried asking our local Apple Genius Bar about this, but they weren't able to help me. Here's the problem:

I've upgraded to Snow Leopard on my late 2006 Mac Pro last year and changed my daily user account from Administrator to User. I run the Stanford Folding@Home on this Mac 24x7, so it is always on and awake. I noticed that I stopped getting notified that Software Updates were available. I regularly check the Internet Storm Center and they announce OS X updates as well as the Microsoft updates. When I run Software Update, I am challenged for my Administrator account and password (as I would expect) after which the program checks for updates and identifies the updates that are available.

My question to the Genius was why do I have to run this manually when I have set the Software Update preferences to Check for updates Weekly and Download updates automatically is checked? I have checked this setting from both my user account as well as my Administrator account and they both show the same settings.

Since then, I've added a Mac Mini running Snow Leopard and I set it up with an Administrative Supervisor account and User accounts for all of the family. The Mac Mini never notifies us of updates, either. Plus, I supply tech support for my in-laws' Macs and they all exhibit the same behavior. This has been around since OS X 10.6.3 (the first version I installed) and every update since. So, obviously, I know how to configure a Mac to break Software Update, but how do I "fix" them to let everyone know that it's time to update the Macs?

Thanks for any help you can lend me.