For the last three weeks, we've been trying to change the schedule of when the daily & weekly portal alerts are sent out for users. The problem is alerts are sent out around 1AM. Using the STSADM.exe utility, you are supposed to be able to set a few properties that specify when alerts can be sent out. For WSS sites, the properties are job-daily-alerts, job-weekly-alerts, and job-immediate-alerts. For SPS, the properties are job-daily-notification, job-weekly-notification, and job-immediate-notification. But for some reason the changes weren't taking effect... alerts were still being sent out anywhere from 11pm-3am. Why was this an issue? We had some people who setup daily alerts and when they were on call, their Blackberry's would wake them up in the middle of the night, just to tell them a document was updated 8 hours ago.
After fiddling with it for a few days with no luck in making any changes take effect, I gave up, and just opened a ticket with MS PSS. After 2.5 weeks, I finally get word that those properties don't work and were never removed from the documentation OR the list of available properties for the STSADM.exe utility. The only way, according to PSS, is to change the schedule of the index crawls as the notifications are sent at that time. So, if you don't want alerts to be sent out in the middle of the night, you index crawls need to be set to crawl in the middle of the day. Getting the feeling this product may have been rushed to market a little too quick.