To possibly answer some questions about the setup, my transparent background blender file uses:
File Format: FFmpeg Video
Encoding container: Quicktime
Video Codec: Quicktime Animation
When I use a similar file that is for animation that dont have a transparent background:
File Format: FFmpeg Video
Encoding container: Mpeg-4
Video Codec: H.264
It works fine in 4.1 and 4.2. So, it appears the issue is with the Quicktime settings. But again, I only have the issue in 4.1 and 4.2. 3.6 has no issues with the quicktime settings.
Thanks again.
