I've just updated Media Encoder to 10.3.0.185, and After Effects to 220.127.116.11 (running on Windows 10). Ever since then, I've been encountering a glitch in the audio of any After Effects projects that I export out of Media Encoder. Everything is fine for most of the video, but as I reach the end of the exported video, the audio begins to double up or cut out and jump to a different part of the track.
This does not exist in the AE project or the original audio track, nor does it occur on any video that I export directly out of After Effects. I've tried exporting with both h.264 and Quicktime, with a variety of presets for both, with consistent results. If I export a video directly out of AE, then re-encode that video in Media Encoder, then the glitch does not occur.
I've been using this workflow without issue for a while now, so I can't think of anything different that I've been doing other than the software update. Has anyone else run into this issue / have any tips on how to fix it?