Not too sure if many realise this, but Keynote animations, transitions and video playback may suffer some lag and "jerks" when presenting on external monitors or projectors. This is assuming that the presentation is on the external display, and the primary display is displaying the "presenter's display." Somehow, this seems to affect the portables more than the desktops.
The solution to this problem is to not display the Time and Timer on the Presenter's Display. This will enable smooth transitions, animations, and playback of videos in Keynote during presentations.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20070411013049667