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Have you tried using the Legacy Quicktime gamma checkbox in your AE color management?
Have yout tried the Levels Animation Preset - Computer->RGB (I think its under Img Utils)
My understanding is that the gamma issues that occur when using Quicktime codecs like ProRes are a fault of Quicktime, not After Effects.
I use 10 bit uncompressed QT files regardless of Standard or High Def, and have no gamma conversion issues. Why do you consider 10 bit uncompressed files to be "a pain in the ***"?
The gamma issue is for sure a misunderstanding problem between apple & adobe.
Does Prores can be seen as faulty when it works like a charm inside fcp or any of the fcp suite software ? I'm not that sure...it may yes, but I just don't know.
Also, Quicktime, even being sometimes dirty, dictates the way to go. It's not an opinion, it's a fact. My workflow is entirely dependent of QT, and AE is a great software but still supposed to handle QT seamlessly, what he doesn't actually...
But my question was more "how to fix it" than "who's guilty"...
10bit uncompressed is just too fast & too big for me.
I have 2x 500Go Huge systems, but disks are not very stable at that datarate, and files are just huge..
Maybe bigger & faster drives would be a solution ;)
Although I am not using the prores codec, I use colour management all the time to correct YUV to RGB levels.
I notice you said you were interpreting footage as HDTV (Rec. 709). I think that may be your problem.
I set the project working colour space to be HDTV (Rec.709) but I interpret the footage as SDTV PAL 16-235 or HDTV (Rec. 709) 16-235. The 16-235 part corrects the luminance level issues and my final output is always correct for Final Cut and also Avid.
Hope this is helpful
FWIW: I am having same issue in Premiere (Adobe Media Encoder) where I export to Apple QT YUV422 24 bit that is then loaded into FCP and Mastered for broadcast via Kona Card.
Images being broadcast are "blown-out".
Looking for a solution and suspect I have to find a Levels Control 16-235.