I'm currently doing experiments with codecs, and of course I'm choosing DXV3 for everything (for performance), despite the poor support for playing outside Arena. QuickTime 7 still works fine, until they deprecate it.
I see that the problem goes away with the high quality filter, and that's ok, this means I've got to check every single clip I convert.
Also there are BIG issues with smoke, probably due to a lower threshold with similar colors, I'll share a screenshot. I'll also post the other when I find it.