This might sound like a dumb response but have you tried deleting the old background layer and remaking a new one in it’s place. If it’s not too much work for you?
A few days ago I had some trouble with a video that included 3d layers. Essentially the video showed a book opening it’s cover with a light sort of creating a gloomy mood.
Everything was fine in after effects like i said, but once i had rendered the video and opened it in quicktime, i had this weird problem where the book cover would become 50% transparent (or at least it seemed that way) just before the cover started to open.
I showed it to all the people i knew who had knowledge of after effects and was told that they didn’t know what was up. one guy just suggested deleting and putting the same image back in and it worked completely fine.
Sorry for the long winded tale, just thought that if i gave you an example of it actually working it might seem like a less amateurish response.
Let us know if it made any difference.