I've noticed the same problem over and over again with various animated banners I've come across, so I thought I would take a moment to explain my point of view.
With a lof of flash banners nowadays, I've noticed various fade in and transition effects come into play. What people fail to do, however, is make sure that EVERY single frame includes the company's logo and (unless it's blatantly obvious) a demonstration of what the site offers.
Banners are mainly used for branding nowadays. And, it goes without saying, that when doing banner advertising on a site, you only have a split section to catch a user's attention before they scroll right down the page past the banner. Do you really want that split second to be just as your logo is starting to fade into view as the fancy animation that offers no informative benefit to the web surfer spirals away??