Java keeps it's time zone data independently from the operating system (at least on linux), if you want to keep it updated you should download Time Zone Updater from oracle(sun)
and then run the command
java -jar tzupdater.jar -u
The user should have permission over the JDK/JRE directories.
More details on http://www.oracle.com/technetwork/java/javase/timezones-137583.html#tzu