I think it might be the Quicktime installation, if you’ve been having problems starting quicktime, at the time you start After Effects it will throw you that message, I uninstalled quicktime and then my after started, of course it told me “Quicktime functions will be disabled because a compatible version of QuikTime could not be found”
Now I have to fix the Quicktime problem but at least I know I don’t have to reinstall After Effects.
I’m running Windows 7 x64