Michael,
Did you ever find an answer to this problem. I just installed CS5 and am having the same problem with Premiere Pro as you posted. When I choose Export, then select Media, then select QuickTime, then select Animation for the video codec, the Codec Settings box is still grayed out. And, when I choose the Animation Codec, I have no way of changing the size of the exported video, either. The output is showing 720×480, instead of the full 1440 x 1080 size of the original sequence, and there is no option available to change it. Am I missing something?
I’d like to use Ultra for my green screen keying (because it’s so stinking easy to use), then export the keyed clips, including Alpha to an Animation file with Millions of Colors +. I can then take that file into Final Cut (my preferred editing system) for further editing. Can’t seem to find a way to do it other than exporting a PNG sequence, which gives me aspect ratio problems in the final file. Any solutions?