When rendering with Adobe Media Encoder, the sound only starts playing at 1 minute and 20 seconds

So I have this problem: I have a video which is an hour long and when I try to render it via AME the result will have the audio of the video starting at around the 1 minute 20 mark. I render to the YouTube 1080p preset.
What I have tried to fix this is:
- use .wav instead of .mp3 (didn't work)
- use After Effects itself to render the video (this worked)
- change the video start time to 1 minute and 20 seconds and then made AME start the render at that (didn't work)
- re-render (didn't work even on different presets)
It's also not my audio file because I've tried rendering it with the audio starting at 1:20 and then the track was playing from the start.
The video contains one audio track and one video and the project file is in After Effects.
Is my AME bugged or am I doing something terrible wrong?
Hope to hear from you guys.
PS: I really don't want to render via After Effects, due to file size.

I'm having a very similar problem. I just purchased a larger SD card thinking it was the card but it's definitely Media Encoder.
Mine is also crashing in the middle of renders and causing my computer to crawl.

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