I've been editing some videos that come from IGTV recording, I always put them through HandBrake before opening it on Premiere to prevent any frame rate problems.

At first everything worked fine and Media Encoder exported it brilliantly (H264), saving me a lot of time. But out of nowhere all of my videos started having audio out of sync problems. The funny part is that is that the audio on the exported video starts as if it were the master video from where I extracted the smaller videos I edit.

I've already tried clearing Media Enconder cache, but it didn't help. Also tried using a different format but the problem persists. It only works if I export it through Premiere and that takes forever since I have more than 10 videos lined up to export.