I just love this:
Apple KB Article.
Thanks Apple. Clearly related to the Quicktime gamma shift that has been in Quicktime for like - well, forever...
I see it all the time if I try to render out of AE. Then you have to apply this:
After rendering into a QuickTime/h.264 file, open it up in QuickTime and select “Show Movie Properties.” Highlight the video track then click on the “Visual Settings” tab. Towards the bottom left you should see “Transparency” with a drop-down box next to it. Select “Blend” from the menu then move the “Transparency Level” slider to 100%. Choose “Straight Alpha” from the same drop-down and close the properties window and finally “Save.”
Apple really needs to fix this. I am going to guess that it must be an overwhelming task to fix it as they have, long ago, acknowledged that it is in issue.