Thanks for the reply, Martin. I ran into this issue a couple years ago when I was rendering a scene in Evee and the render speeds were under a second. It caused the sequencer to get a few frames out of order until I changed it to use the PNG name. So, I am familiar with the fix. And you are right, it isnt the issue I am having.
Out of curiosity, how do you sequence a video from PNG files to produce a video with transparent backgrounds if you dont use the Quicktime settings? I have always used them because early on I saw a video that suggested this was a good solution. But I am not married to it. I do all my video editing in Final Cut Pro, so the Quicktime settings work well there. But if another Encoding Container and Video Codec would produce a video with transparent backgrounds, I could give that a try.
Thanks again!