It looks like this is a Java bug rather than a kernel problem.
TTL works correctly in the early-access version of Java 7.
$ java -version
java version "1.7.0-ea"
Java(TM) SE Runtime Environment (build 1.7.0-ea-b22)
Java HotSpot(TM) Client VM (build 11.0-b08, mixed mode, sharing)
For pre-Java7 applications that only need IPv4 try
-Djava.net.preferIPv4Stack=true
For applications that needs IPv4 and IPv6, iptables can be used to force
the TTL
iptables -t mangle --append POSTROUTING --out-interface eth+
--protocol udp -j TTL --ttl-set 64
--
TTL ignored when sending UDP Datagram to IPv4 address via IPv6 socket
https://bugs.launchpad.net/bugs/112257
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