I usually move the VLC window to the top-left corner of the screen. When I tried to open the Effects and Filters window on 1.1.0-pre3, at first I thought I wasn't working but then I realized that it was actually opening it but the window was off the screen.
It can be solved if you open the Effects and Filters window at least once before moving the main VLC window so that it remembers its position, but it still seems to me kinda like a minor bug for it to -potentially- have windows appear offscreen.