After upgrading to TIBCO BusinessWorks (BW) 5.10 (most likely not related) and TIBCO Runtime Agent (TRA) 5.7.4, JDBC connections using the Microsoft SQL Server JDBC driver (com.microsoft.sqlserver.jdbc.SQLServer - sqljdbc4.jar) times out. This happens for example in the TIBCO Designer when using "Test Connection" on a JDBC Connection.
Note that TRA 5.7.4 includes JRE 1.6.0_30.