Java 6 update 29 introduced a fix for the vulnerability known as BEAST which affects connectivity with certain versions of SQL Server. See the link below for more information and SQL Server interoperability enhancements provided by Microsoft.
http://blogs.msdn.com/b/jdbcteam/archiv ... te-30.aspx
In the 4.3.0 upgrade of GoAnywhere Director, the Java Runtime Environment will be upgraded to 1.6.0_38. If you experience connection failures with SQL Server after upgrading GoAnywhere Director to 4.3.0, you will either need to apply the SQL Server patch provided in the link above (recommended), or downgrade your JRE to a version prior to 1.6.0_29.