Jonas Hummelstrand’s great blog, General Specialist, had these excellent tips for fixing problems with After Effects.
Here is an excerpt:
Having problems with After Effects? Here’s a collection of tried and true remedies:
1. Check that your system harddrive and the harddrive where you store your After Effects project and footage aren’t full, and then run a disk check to make sure they aren’t damaged.
2. Uninstall QuickTime, restart your computer.
3. Uninstall any third-party video and audio codecs for QuickTime and Windows Media, such as XviD, DivX, FFDShow, BlackMagic, Aja, Avid, Flip4Mac, etcetera.
4. Reinstall the latest version of QuickTime.