Hey guys,
It’s been a while since someone respond to this thread but I had the same problem than Mark. Clean footage coming from FCP was pixelated when imported in AE. I tried to export my clip from AE, and then it came out clean as the source footage. So the problem was in AE.
It appears that it is a preference of the viewer which sucks. Go into Preferences > Previews. Then you can change “Zoom Quality” from “Faster” to “More accurate”. And then, everything go back to normal in the viewer. At least it was my case.
I hope it can help someone.
Cheers.