A long project, huh? Did you use Open GL to speed up rendering? Don't. Doing so is the prime suspect in rendering weirdness like that. Sorry it's such a long render, but NOBODY uses Open GL to speed up the process, for reasons that may be painfully apparent to you.
Thanks for the reply but I don't use Open GL when rendering...only when working in a comp for previews.
One suggestion I received on CreativeCow not to use the H.264 in AE...
It's just strange that I used the same file the client was having problems with, compressed it again with Handbrake, and then it was fine. So maybe I'll just render a lossless .mov out of AE and have to use Handbrake to make the mp4. It's a pain but at least it worked in the end.
Yeah, that's weird, all right. AE's not the best thing in the world to use when rendering to H.264.
In addition to Handbrake, Adobe Media Encoder will also make H.264's from lossless files. As will QT Pro, and many other applications.