In Java 6u29, there was a bug introduced which prevented SSL connections to SQL Server 2008 R2. This bug was logged with Oracle as Bug ID: 7103725 here :
Oracle has delivered a fix in 6u30, although some claim it still is not fixed. This bug is primarily effecting OSX users because of the Java Update to 6u29. Users can get around this bug by passing Java the property "jsse.enableCBCProtection=false" with the flag :
Attached is a screenshot of how to change the /Aqua Data Studio/Contents/Info.plist to add this flag. Once this flag is added the SSL connections to SQL Server will work.