When you following the Microsoft's Best practices for installing and set different application pool account for each application pool, you will get an error when activating a feature with webconfig modifications.
A quick work arround for this is to temporarly change the application pool account of the webapp from which you will activate the feature, to the same account as the central admin webapp.
This is because the central admin application pool account has specific permissions on stored procedures on the sharepoint_config database,which are required to run the update.
Links to the Best Practice Guides
Office SharePoint Server security account requirements
Installation guide for Office SharePoint Server 2007
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