As of SQL Express 2008 R2, installing a default instance (not named) requires manually naming the instance to “MSSQLSERVER” for a functioning server on the default port.
This problem is documented at http://www.kendalvandyke.com/2009/01/installing-sql-express-2008-as-default.html – bug still exists in the SQL 2008 R2 Express installer. Workaround is fairly simple, just use “named instance” of MSSQLSERVER during setup.
Another important note, use “SQL Server Configuration Manager” to enable TCP, Shared Memory, and Named Pipes connectivity on all SQL Server instances and clients on the server. This will allow standard connectivity for Java JDBC, SQL Native Client, and other vital application connection methods.