I was having no luck importing AIFF files into After Effects CS3 on my new Macintel. It could be that rather than reinstall all of my software on my new Mac Pro, I used the migration assistant to transfer all of my files and apps from my G5. I believe that was my problem.
The solution: Uninstall After Effects using the installation disk, and then reinstall.
Works as it should now. Hope that works for you.