Importing movie file - transitions don't work?

Hi all, this is my first post. I searched a bit here and EVERYWHERE on the internet, but couldn't find a solution to my question.
I'm trying to import a .mov file I created in powerpoint. In the file there are smooth transitions, where one images fades into another. When I import the file, I can view the movie in the preview window (double click the filename in the Project tab). It plays fine, all transitions are intact. However when I drag it into my composition the transitions are gone and there is no fading. It's like there is an alpha channel that's not getting interpreted correctly. I've tried every setting in the Interpret Footage window for the Alpha channel.
I've done this in several other projects. It's always a pain to get past this part. For some reason I can never repeat the same steps to get it to work.
If anyone knows what REALLY going on and what I can do to import the footage properly, I would appreciate the help.
Thanks!

Todd_Kopriva wrote:
> It's still puzzling that I can play the movie fine in AE's preview window :/
What version of After Effects are you using?
When you say "preview window", what panel are you actually referring to?
If you're referring to the player window that opens when you double-click a QuickTime footage item in the Project panel, then you need to know that in After Effects CS4 and earlier, this is just a QuickTime Player window.
Ah, that makes sense then.
I'm using CS4.

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