You will loose your good playback rate by adjusting the movie settings after render.
From my experience i never render h264 straight from AE unless the look of the end result doesn’t matter. There is a plugin for Quicktime Mac that can encode h264 without problems, Perian http://perian.org/ i believe it’s based on the x264 library which other encoders utilize as well http://en.wikipedia.org/wiki/X264.
I also know that encoding with Quicktime can sometimes produce different gamma results depending on the material you encode. I think there is a difference between PNG and TGA for example were quicktime for some reason consider one of them to be in linear gamma space, and there is no way to set sRGB manually.