Adobe’s yeoman After Effects documentation guru Todd Kopriva maintains a highly useful blog over on Adobe.com.
Today he just posted instructions on how to modify the After Effects CS4 QuickTime gamma rules XML file (did you even know such a thing existed?) to allow proper round-tripping using ProRes4444 without getting those gamma shifts that cause many of us to rip our hair out.
The post also includes links on how to make ProRes 422 roundtrip, and general background information on gamma shifts and After Effects.