Directly from the xdotool manual:
SENDEVENT NOTES
If you are trying to send key input to a specific window, and it does not appear to be working, then it's likely your application is ignoring the events xdotool is generating. This is fairly common.
Sending keystrokes to a specific window uses a different API than simply typing to the active window. If you specify 'xdotool type --window 12345 hello' xdotool will generate key events and send them directly to window 12345. However, X11 servers will set a special flag on all events generated in this way (see XEvent.xany.send_event in X11's manual). Many programs observe this flag and reject these events.
It is important to note that for key and mouse events, we only use XSendEvent when a specific window is targeted. Otherwise, we use XTEST.
Some programs can be configured to accept events even if they are generated by xdotool. Seek the documentation of your application for help.
Specific application notes (from the author's testing): * Firefox 3 seems to ignore all input when it does not have focus. * xterm can be configured while running with ctrl+leftclick, 'Allow SendEvents' * gnome-terminal appears to accept generated input by default.