Try inserting a pause:

use Win32::CtrlGUI;

my $window = Win32::CtrlGUI::wait_for_window(qr/Notepad/);
sleep 1;
$window->send_keys("!fx");
[download]

I had a similar problem, with an application that was taking too long to finish drawing it's window.

If you had the same problem, you would have to check if specific fields inside the window are already drawn before sending keys.