This is really weird. I have *no* idea what could be wrong in After Effects. My first thought was that it was treating everything as sRGB but "linearizing" with gamma 2.2, which causes a discprepancy in dark colours, but when I adjusted for that in Nuke, it made for a much much bigger difference. It's really just the foliage that's different between your images, and any kind of incorrect colour math produces a massive difference everywhere.
Frankly, just buy Nuke or Fusion. Or dig out an old Mac and look for a copy of Shake. Almost anything is better than After Effects for comping.