I have been encountering this problem as well and have found that it seems to be related to our EditShare storage system. A test project stored on the local hard drive with the same footage was able to complete a render with no issues.
Running the project with the media stored on the server causes the “Not Found” error when rendering finishes, leaving the footage unrendered.
The problem only started occurring when we upgraded to Leopard. I am hoping to solve our issue with a server software update.
Could your issue be related to how/where the media is stored? What is your workflow? When did you first encounter the problem? After any updates?