Yup, the Ubisoft logo tricks the ATI card into thinking its running a flash game essentially because the movie is played by a flash player which is not usual for games which normally use a video decoder such as Bink instead. Deleting it lets the card detect the game properly, as well as giving you a much quicker menu loading time.
The file might be redownloaded with future updates through Steam so you will have to delete it each time.
As for questions to whether the bug is still around or not, I no longer use my old HD4870 which did get it so I can't confirm. The newer HD6000 series cards don't seem to suffer from this issue but I delete the logo anyway just to be sure.