This appears to be either a bug in the gnome screensaver or SDL; SDL is supposed to disable the screensaver while an application is running in fullscreen mode. It appears to use the XSetScreenSaver command correctly, so I'd blame the screensaver: The gnome screensaver appears to be an external program that ignores XSetScreenSaver changes.
As a workaround, I let the game NOT iconify itself when it receives the deactivation event.
This appears to be either a bug in the gnome screensaver or SDL; SDL is supposed to disable the screensaver while an application is running in fullscreen mode. It appears to use the XSetScreenSaver command correctly, so I'd blame the screensaver: The gnome screensaver appears to be an external program that ignores XSetScreenSaver changes.
As a workaround, I let the game NOT iconify itself when it receives the deactivation event.