Exporting from After Effects through Media Encoder corrupts audio (causing clicks and pops)

Hi. I am using AE 2025 and ME 2025 on Windows 10.

I was noticing some drops in image quality when rendering in After Effects so I decided to attempt using Media Encoder instead. At first my video seemed pristine once it finished rendering, but upon taking a closer listen, I notice that around the midpoint there is some clicking and popping at certain instances, like you might hear from a dirty or worn vinyl record, or from audio that seeps too much "into the red," aka clipping. As the video goes on this seems to be more frequent of an issue. (Note, these sounds are perhaps not easily noticeable to the average listener, but at louder volumes or perhaps on a second listen it is probably noticeable. Given that the audio for this project is music, this is rather unoptimal. More or less rubbish even still.)

This is very upsetting, after waiting a fair amount of time for the video to finally render, after having to restart to fix some issues on my end. However, I am fully confident this is the fault of ME, because my original mix audio file that I used for the video does not have these clicks and pops at the same timestamps (nor at all).

I rendered the video with H.264 and standard/default settings otherwise (w/ AAC). How can I fix this? How can I prevent this from happening again?

I saw much older posts similar to this with no solution beyond just exporting directly from AE or Premiere, which makes me wonder the purpose of using ME. I find these solutions unpreferable, as like I said, I found ME to retain more visual quality than exporting from AE directly.

Thank you.