First question -- are you getting a good key? Hope so.
I recommend Prerendering the chroma key shot. Just put the clip in its own comp, pull they key & render to a video container & codec that supports alpha channels. For this task I like quicktime movies in JPEG 2000, PNG, Animation or ProRes 4444(if you have it).
Use the AE RenderQueue. In Render settings set to Best Quality. In the Output Module set to one of the above codecs, RGB+Alpha, Millions of Colors + and Straight, i.e. NOT Premultiplied.
Then import into AE, add to your master comp, and mess with Timewarp.
What Dave said. You have to read up on how AE processes stuff based on its rendering order and how specific effects work. If you were to re-time your stuff, you would have to do it before keying to avoid the issue.
Are you still facing this problem? If not, let us know how you solved it. If so, please let us know so we can assist you further.