[Andrew Brown]

Replying to an ancient post in case somebody else finds this useful;

I was haunted by the same problem, in ever-increasing degrees, for a long time. Render glitches persisted, irregardless of the source material for the projects; different video footage, generated purely in AE, etc. People more knowledgeable than me suggested the following, which I did:

Render to a hard drive, not an external drive
Make sure there is ample space on that hard drive
Set AE to clear the cache every set number of frames during renders
Check your OpenGL settings
Etc., etc.

Nothing worked. The thing that finally solved the problem was switching from rendering .MOV files in animation codec, to rendering .MOV files in PNG codec. Hundreds of renders later, and glitch-free.