I ran into this very problem trying to send mail with javax.mail from a web application in a web server running Java 7. Internal mail server destinations failed with "network unreachable", despite telnet and ping working from the same host, and while external mail servers worked. I tried
System.setProperty("java.net.preferIPv4Stack" , "true");
in the code, but that failed. So the parameter value was probably cached earlier by the system. Setting the VM argument
-Djava.net.preferIPv4Stack=true
in the web server startup script worked.
One further bit of evidence: in a very small targeted test program, setting the system property in the code did work. So the parameter is probably cached when the first Socket is used, probably not just as the JVM starts.