I recognized additional differences between fullscreen and windowed mode on my computer:
In fullscreen mode with vsync turned on the mouse cursor seems to be moving a bit slower than in the windowed mode or with vsync turned off.
Furthermore i tested some WME games using 2D actors and noticed that if nonplayable actors/entities turn around (for example in a cutscene) they sometimes flicker shortly while turning. This only happens if i use fullscreen mode and turned vsync on. If i use windowed mode or turn vsync off everything works fine.
But as you stated before turning vsync off cannot be the answer because this leads to half-screen flickering (for example when the screen scrolls).
In order to see if these problems occur only on my computer i tried it on an other computer. But there i had exactly the same problems.
I also tried a few fps settings for my ogg-video as you proposed but sadly this didn't bring any advantage.
Now, i don't know what to do to solve these framerate problems.