I am getting a really serious color shift in Adobe Media Encoder as well. I am not sure how to handle it. I can go between FCPX and AE with no problem but when I try to export a final rendered file out of Media Encoder it increases the saturation and also shifts the color. I have been fighting this for over a year and a half but I am stuck with Adobe media encoder because we are producing .f4v’s with meta data embedded. I also get a color shift in Premier when I bring things in from FCPX. I have tried to find an answer but all I find are people saying that it is a Quick time problem. The problem with this answer is I go between multiple programs with no color shift until it get to Adobe Premier or Adobe Media Encoder. I can go to AE, Davinci Resolve, Compressor, Motion, FCPX, I have consistent color until I get into Adobe Media Encoder which I would just walk away from at this point except I don’t know of any other way of producing the .f4v files with embedded meta data.
Any ideas would be great.