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I believe that you can work around this by explicitly specifying the object owner in the DDL for the stored procedure. SQL Compare creates the object using the original creation DDL in the syscomments table, so if you double-click the stored procedure in Enterprise Manager and see CREATE PROCEDURE X instead of CREATE PROCEDURE [dbo].[x], then SQL Compare will create the SP with the ownership of the currently logged in user.
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SQL Compare handles connection behaviour the same way that SQL Server does. If you connect as n named user who is not a member of the dbo role, the objects will be created as that named user. One solution is to make the user a member of the dbo database role. From then on, these objects will be created with dbo ownership.