I have a couple Prores 4444 files that were exported from FCP. When I try to import them to AE CC 2015, alpha options in the interpret footage window are greyed out and no alpha shows in the viewport. Playing the file back with OS X Finder's Quick Look clearly shows an alpha channel. I found that older CS5 versions had an issue with this, and that it was fixed with CS5.5, but couldn't find any info on this happening with newer versions. I've never had CS5, or CS5.5 on this machine.
Uh-hun..... and what AE and OS versions are you currently running, right down to the last decimal point?
And since media players are typically incapable of displaying alpha channel information, it would be interesting to know how you determined it was there.
After Effects 184.108.40.206
OS X 10.11.1
If I open in Quicktime/VLC, it shows a black background and as expected. If I select the file in finder and press the space bar, or click the quick look button, I see the alpha channel. Finder's quick look shows the alpha channel on most files that support alpha and/or transparency.
I just did a test with a video exported from AE set as RGB+Alpha ProRes 4444 and the alpha channel was interpreted correctly upon import back into AE. So, it must be some export setting in FCP. But of course, I didn't export the video. I don't even have FCP on my machine.
This is an example of Finder's Quick Look function correctly showing an alpha channel. You can see my beautiful desktop image with some OS X gaussian blur shining through. This is not the content I'm working with, since I can't post that here. However, the video in question does display with an alpha channel when viewed this way.