You should not be using Quicktime H.264 at all any more. Apple stopped supporting and developing the container a while ago and it's buggy. That's your biggest problem. Use AME multi pass and render to MP4 if you want h.264 compression. It's a much better format.
Thank you Rick! But AME and AE are using both Quicktime container. So why does it works in AME en not AE?
I did not know Apple stopped supporting this Quicktime container. I can't find anything on the internet saying it did...
This website shows it is supported: Media formats supported by QuickTime Player - Apple Support
Why use MP4 then? Why is it 'better'?
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You shouldn't be using QT in AME either. You should pick h.264 and render an mp4.
QT h.264 in Render Cue is busted and has been removed in the latest versions of AE. It's not a good format. Never was.
Is it better to use AME when I render my projects intead of the AE?