Why Microsoft choosed to release MDT 2008 Update 1 with a known superbug in it I don't understand... but  I don't work for Microsoft so I guess I shouldn't...

Anyway, the MDT 2008 update 1 will wipe your deployment point(s) settings completely... make sure to backup the deploy.xml file before applying the update, by default it's in the C:\Program Files\Microsoft Deployment Toolkit\Control folder...

What to do if I don't have backup, and my settings are gone?
Well, don't panic just yet, as long as the deployment point folder is still intact, you can have MDT generate a new one for you by creating a new deployment point and set the path to the original folder.