There was a bug introduced shortly before we released version 5.2 of Quest Web Parts. The Editor for SI Web Part Catalog property for SQL Server type system does not look into the User ID and Password properties to build the connection string. So if you use Configuration Editor to define the System/Service for SQL Server and enter the User ID and Password in separate box (masked input for the Password), the Editor for Catalog property ignores them and uses the connection string without thus having problem building up the dropdown list for stored procedure.
The bug was fixed and released as 5.2 hot fix since 2010.04.01. However user can chose not to upgrade but work around by specifying User ID and Password directly in the connection string input box separated by semicolon. The problem though is that Password is plain text in the configuration file as well as in the Editor tool.
The bug only affects the Editor for SI Web Parts Catalog property when defining operations to SQL Server.