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Java will display the time set on your system.
I am guessing Ubuntu is not set to use "Automatic Daylight Savings Adjustments" or not set with appropriate "Time Zone".
Best solution for this would be to setup a NTP server on one of your boxes in your network, and configure rest of machines to
use this NTP server.
So you may want to look in to configuring NTP server and Client.
When java starts on a unix box it uses a rather complicated process to determine what the correct timezone is. Windows is a bit simpler although not trivial.
Whatever that process is it isn't succeeding on your box.
There is either formal or informal documentation on that process somewhere. But I don't know where.
You could also figure it out by looking at the source code.
I don't have Ubuntu. But if you are running the latest version it should have new Tzdata files as per new DayLightSavings time.
And if I remember correctly the new DayLightSavings is adopted in 1.5 itself. So I am positive the 1.6 will also have it.
You can check if Linux is set with correct DayLightSavings by running following command. Make sure YOu see Mar 9 and Nov 2
$ /usr/sbin/zdump -v /etc/localtime | grep 2008