Trouble in Ubuntu land

To be able to run several simulations simultaneously, I tried installing RedHat Linux 9.0 on a couple of machines. One was a newer Core 2 Duo machine which had a hard drive interface that RedHat Linux 9.0 couldn't recognize, so I earlier gave up on that machine and installed on an older machine. However, JVM kept crashing on that older machine. So, I installed Ubuntu 8.04 after downloading it from the neighboring machine. I then installed JDK 1.5 update 15 and ANT 1.6.5 followed by building of TOTEM simulator. However, when I ran the simulator, the simulator window was restricted to the left half of the maximized application window. There were also some exceptions on the console. I searched for the reason and found this page helpful. I downgraded the X library as suggested on that page and everything is working fine now. I do get some exceptions in some simulations sometimes, which I am trying to track down and eliminate. Ubuntu is running pretty nice.