Q. When I deploy System Center Update Rollups, why do I have to manually run SQL update scripts for some components?
A. Some Update Rollup instructions include steps to manually run SQL scripts on the database server. The question is "Why can't the update process automatically run these scripts instead of requiring users to do the work of manually running them?"
The biggest reason: Windows updates run as LOCALSYSTEM, which would have no permission on a SQL database. Therefore, the SQL updates need to be executed by a user with sufficient permissions.