This topic has always been a sore subject with customers and Altiris when it comes to using Deployment Server. The feature is available when using Notification Server to run something as the logged in user in order to make settings withing the users profile. With Deployment Server, you did not have this option. The options were to run using the system account or specify a user only, not use the logged in user context. One of the ways that you can get around this is by using PCTransplant. Create a template containing the information that you want to capture. Create a personality package on a machine with the settings you want to capture using the template you created. Once the package is created you can deploy the package to the target computer missing the specific user profile settings by adding the PCT Switch option -user:'options'.
Example to deploy package to all domain users on a computer silently:
myprofilepackage.exe -user:\mydomain\* -q
The trick here is that when creating a personality package from the template, you are logged into a computer with a domain account that has access to the computers you plan to deploy the package to.