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How much RAM do you have and what's your disk setup? Such issues point to bottleneck situations where the footage cannot be properly loaded by all the instances. This issue is mostly unrelated to AE and merely a resource problem in QT itself. Only fast disks and lots of memory help to overcome it.
10 Gigs of RAM (AE is set to use 4 CPUs)
Standard SATA Drives - no Raid
There are only two Quicktimes and a bunch of stills involved in this project - can't imagine that disk performance is the bottleneck here.
Are you using QuickTime reference movies? When you open the project are any of the movies offline?
There were some bugs related to these areas, some of which didn't get fixed until After Effects CS4.
If you do have missing footage, relink them on project open then save, close, and reopen the project. If you're using reference movies, make sure that all of the referenced files are present and accounted for.
Sometimes changing the project settings or a project-related preference will cause After Effects to reload the files and kick it into gear.
No footage is missing and no reference Quicktimes are used. The placeholder just flickers in on a few random frames of the rendering - without multiprocessor rendering all renders fine.