SQL Packager creates databases in a way that is compatible with the database being packaged. For example, if the database resides on the SQL 2000 platform, the database scripts will be created in the SQL 2000 syntax. If Packager is configured to create an "upgrade" package, then it can change the T-SQL syntax so that it conforms to the target server platform.
To create a database package using the SQL syntax different from the version of the source database, it is necessary to have an installation of the version of SQL Server that you would like to deploy to.
SQL Packager will produce a script to create all objects in dependency order, and use syntax that is compatible with the target server platform.
Where possible, new features such as CLR assemblies are filtered out because they are incompatible with SQL Server 2000. Sometimes this is not possible, for instance if a stored procedure relies on a CLR function. Since the function cannot be created, the stored procedure cannot be successfully scripted. Analyzing your databases for these conditions first is recommended.
If you continue to experience problems, please contact Red Gate Support.