If you run the installation program for Cumulative Update (CU) 2 for System Center 2012 SP1 Configuration Manager (ConfigMgr) with insufficient permissions on the SQL Server you get a warning on the step "Perform Database Update" in the wizard.
If you click on "Show log file" the following message is displayed: "Task status detail added: A SqlException occurred, Line Number: 44Error: 229 Message: The EXECUTE permission was denied on the object: <?>, Database <?>"
This because of missing permissions on the Master & ConfigMgr database, so just choose another account with required permissions or add permissions to the already used account. After that the SQL script must be started manually.
The SQL script (update.sql) can be found in the hotfix folder in the installation path for ConfigMgr on the Site Server where you started the update. Just copy that one to the ConfigMgr Site Database Server.
Start SQL Management Studio after that, choose the right database above and open the SQL script. As mentioned in the SQL script the SMS_EXECUTIVE service must be stopped on the ConfigMgr Site Server before running. Click Execute and you're done!