Hmmm, an interesting problem. I have only ever had this reported when it comes to alpha masks for videos, but generally speaking the difference is that you either have one, or you don't. It's possible that the actual file format of the video makes a difference. I'm using webm, so maybe it makes a difference for mp4 or something along those lines. I don't get these issues at all though so it's quite hard for me to test.
Ren'Py is meant to handle garbage collection by itself, and unfortunately doesn't have a massive amount of tools to debug something like that, but what I may do in future to avoid this is just create an ATL version of the same animation (Basically a simple version that can be played as an alternative) that people can swap to if they start to get issues with the animation on their system. It's one of those things I could probably pour 20 hours into and not fix, so instead I think I'll just make a setting to allow people who get the issue to essentially disable it. I'll likely do that for 0.23. Thanks for the report, and I hope that aside from the flashing issue that you've been enjoying the game so far.