Thanks for all the replies. I need to switch my notifications on as I missed these!
So I discovered it was from a legacy setup with how my movies were working before: In the project settings ‘Exclude Movie Files When Staging’ was checked, with ‘specific movies to package’ enabled.
Unchecking that and repackaging the project got it all working! It enabled the bk2 movies and they also work on the Steam Deck 
FYI I’m using 30fps bink movies and they work great.