Resident OCD AE gamma geek here. I've had a lot of trouble reproducing this problem lately with Quicktime Uncompressed 10bit as the original source in FCP(which is then converted to ProRes4444 in FCP), but I can now easily reproduce with ProRes4444(when it's re-rendered to ProRes4444 in FCP).
I'm not sure why I can't reproduce with ProRes4444 media that was originally 10bit v210, but in the meantime, here's a solution that *should* work for most of you.
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Add the following line to your MediaCoreQTGammaRulesCS4.xml file located at harddrive/users/username/library/application support/adobe/common
<QTCodec codec='ap4h' vendor='****' platform='mactel' direction='encode' versionlow='0x00000' versionhigh='*' gammatag='true' />
We've already got the rules for the other flavors of ProRes, so this is a safe change. It just adds the appropriate tagging for 'ap4h' which is the 4444 flavor.
Thanks,
Dan Ramirez
After Effects
QA