In my GUI I have blank space as well. JToolBar has a nested class for tool bar specific separators, but it doesn't appear to have capability to set separators or make them visible.
The result is the same with each of the following examples...
From the 1.4 API...
public static class JToolBar.Separator
extends JSeparator
A toolbar-specific separator. An object with dimension but no contents used to divide buttons on a tool bar into groups.
I guess since it has no contents it has nothing to display.
Since you are using the JSeparator class instead of the JToolBar.Separator class, have you tried using JComponent's
setPreferredSize( Dimension d ) method?