When using a setVisible(true/false) on a window on Linux using J2SE 1.3 the native code does not seem to set flags consistantly and the outcome is varied pending on the window manager.

Under KDE the window does show/hide.
Under Enlightenment the window will show every other call to setVisible(true)
Under FVWM the window will not show apart from the initial setVisible(true).

The window enters an iconic state when it is re-mapped, and hence does not show.