Here's my process if that helps:
Never had a "film" or any bubbles worth mentioning on 2nd ferment. I wouldnt shake the bottles, but I occasionally turned them to see if there was sediment on the bottom.. and I didn't do that for any reason other than to check out my fermentation babies, so it probably didn't help as it wasnt part of my normal routine (so I'm sure I missed batches of flipping them).
Sorry that might not have helped much but maybe you can look at what you're doing in comparison to the process I've used on maybe close to 40-50 batches over the last year and see if there's anything glaringly obvious
I use those glass jars with the rubber seal. It doesn't that any air-tighter and it looks decent as well. You won't be able to fit as many as in a tupperdor but it would look better and has a better seal.
https://www.amazon.com/Bormioli-Rocco-Glass-Canning-Italian/dp/B001AFL8MI