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I am currently having the issue where After effects won't render the audio at the last frame with mp4 codec even tho it does render audio with mov codec.
The bottom brown layer is the composition and the top blue one is the one I exported via Media Encoder and you can see that the audio is missing at the end.
Any kinds of help or advice or suggestion would be appreciated.
Does it happen to all the media files that you import? What's the exact version of the After Effects and Media Encoder you're using? Also, what are your system specifications (CPU, GPU, RAM, OS version)?
We're here to help, just need more info.