The twitch vod->youtube uploader seems to have a minor bug and doesn't currently seem to always keep them in sync. I have heard that they are blaming OBS for this, but let's look at the facts: Twitch vods created by OBS are in sync. OBS' file output is in sync, and when OBS-generated video files are uploaded to youtube, it is in sync. The only time it goes out of sync is in twitch's youtube uploader. There has to be some sort of miscalculation/minor bug in their uploader that is not processing the packets correctly.
If there is something wrong with the transmission of OBS itself (which technically there isn't), then they are not relaying the issue through the proper channels to relay me what specifically I need to do to fix it. I can't really know without them telling me. I have a theory of course, and it's the their twitch->youtube vod uploader expect all audio packets to be pretty much perfectly seamless in terms of timestamps, and aren't accounting for audio packet time shifts properly, but that's just a theory. Without them telling me specifically, I'm just creating workarounds for theoretic bugs in their own utility. Which I -am- doing because I have no choice, but still, it's a workaround to a theoretical bug in someone else's utility. Not the best situation to be in.
