The theory with the ubi video is two-fold; in that the codec used to play it back locks the display to a 'windowed mode' even after the game proper has started. Display drivers try to control heat/voltage for your video card and will 'underclock' it to use less power when it thinks you'll just putsying around in windows
On ATI (which I think is where people see improvements on this) you can use a utility to check this like GPU-Z, i.e. http://www.techpowerup.com/downloads/2120/TechPowerUp_GPU-Z_v0.6.0.html
The second tab shows the GPU core clock speed, which (dependant on card) show different speeds. The theory is that deleting the ubi video then stops it from playing, allowing your game to run at full clock speed.
Here's mine now - in a game it should run at 900 MHz or so, so here it is in Windows at 450MHz:
The second theory is that anything Ubisoft touches is cursed, which is why when you see the logo your game will run worse.