The doubleclick time in Java applications should be read from GTK or KDE settings, but aren't.
I had this problem since I use Gnome 2.10.2 on Debian. Sun has a bugreport on this.
The solution is to add the following to ~/.Xdefaults:
xrdb -merge ~/.Xdefaults
to merge the newly created settings into the running X server. Settings will apply at next Java app. startup.
You can replace 500 with a number in milliseconds that you wish to set the doubleclick time(out) to.