There is nothing so frustrating as unexpected Gamma shifts. Round tripping between AE and FCP when using ProRes 4444 you may notice a gamma shift when bringing exports from After Effects into Final Cut Pro.
To avoid this gamma shift, you’ll need to edit your After Effects CS4 QuickTime gamma rules XML file. This will add the appropriate gamma tag to your QuickTime files on output.
The XML file is found here:
[hard drive]/users/[user name]/Library/Application Support/Adobe/Common/MediacoreQTGammaRulesCS4.xml
Add the following line to your MediaCoreQTGammaRulesCS4.xml file:
<QTCodec codec='ap4h' vendor='****' platform='mactel' direction='encode' versionlow='0x00000' versionhigh='*' gammatag='true' />
‘ap4h’ is the 4cc code for ProRes4444. You’ll notice that the XML file already includes entries for ‘apcn’ and ‘apch’. These are the 4cc codes for the older flavors of the ProRes codec.
Once you’ve made this change, you should be able to round-trip ProRes4444 media between Final Cut Pro and After Effects without experiencing a gamma shift.
More info here