I sounds as if there is something in your environment that causes the issues with Java. We haven't heard about the kind of problems you experience from others on Linux. Have you tried with another window manager?
What version of DbVisualizer are you using and what Java version?
As soon as I start creating a new DB connection, the entire X system freezes: can't transfer focus to any other window, the on-screen clock does not refresh, cannot close or move any window, the only thing alive on the screen is the mouse.
The only way out of this is to logon to a terminal screen (by pressing Control+Alt+F1) and kill the DbVisualizer process - then everything unfreezes and the whole system seems to be back to normal.
Has this been observed ever before? How should I troubleshoot the problem? Any ideas are welcome.