Ben, create a copy of the scene, so we can explore it further.
Please replace the Texture with a Checker-board shader, so we exclude the path or any other problem.
(I switched to “Seen by Camera” and I was able to see all four parts that have an alpha.)
Let me ask you this: is the alpha channel missing on the objects or do you miss the alpha in the quicktime that you render out?
If it is the in the QuickTime, you have set the output to Straight alpha, but not a separate, which I would always prefer (Well, I use image sequences…)
https://www.amazon.com/clouddrive/share?s=pqWGk2KcS0Uh34UI0zrzgU
Let me know if that represents the files with the problems. I have excluded any other non-alpha. If this is the result you are looking for. I have attached as well an Images of the files I have in use. I placed them all on one layer and switched to solo, which excludes of course some influence…
As a siden note, I have no idea what is going on—on your side, So perhaps Support should be considered. it’s 2pm here.