I've run into this issue with ProRes4444 source files inside FCP X. The file in question has mixed alpha conditions. The first segment in the file is a reference composite of animation over video. This is followed by the animation clean. This pattern is repeated for a series of animation clips.
The files was exported from the client's FCP X (all clips as primary storyline clips, not connected). When I preview the file using QuickLook, I can clearly see that the sections of just the animation have an alpha. But when I try to key these as a connected clip over video in FCP X, it does not recognize that there is an alpha there and I can't change it in the info pane.
The client re-exported only the animations without the reference composites and these keyed fine and FCP X recognized that there was an alpha in the file.
My guess is that if your file is mixed, like the first export, FCP X won't recognize the alpha, because the first clip in the file doesn't have an embedded alpha. I presume this is a bug. Thoughts?