I've written in th past about the difficulties I've encountered when attempting to encode video in any non-standard format using the encoder that came with Adobe After Effects. This is just a quick heads-up to let you know that this seems to be fixed in CS6, where the encoder now is far more cooperative when encoding in odd frame sizes. It still doesn't have all the handles of a dedicated encoding solution, but it at least allows you to encode in the format you need.
Case in point, today I encoded a 1312 x 1200 H.264 video without any trouble. That was not possible in CS4. Al least I couldn't figure it out. (I don't know how this was handled in CS5/5.5, since I never used that version.)
Mike