Please check the version of the newly created SQL Server database files.
Attach the database files in SQL Server Management Studio, right-click the database name, choose Properties, then check Compatibility level in the Options tab.
If the Compatibility level of the newly created database files is "SQL Server 2005 (90)", I think maybe there are both SQL Server 2005 Express and SQL Server 2008 Express on your machine.
If so, please try to modify the SQL Server Instance Name in Visual Studio 2008.
Go to Tools -> Options -> Database Tools -> Database Connections, fill the SQL Server Instance Name with the name of SQL Server 2008 Express instance. Then create a new database in Visual Studio 2008 and check its version to confirm.