Audio shifted half a frame early (848 samples)

I have been using watch folders for DNxHD and H.264 transcodes, as well as stripping audio. Seems like anything I run through media encoder that outputs uncompressed audio is shifted about half a frame early (848 samples) compared to the original. I have recreated this issue across multiple systems, even with new presets made from scratch. This has been the case for a long time and it's consistent. This doesn't happen with my preset that outputs AAC audio, but it does happens when I output only WAV audio files (no video), or a DNxHD video with uncompressed audio (that's all I've tested so far).

This is a huge problem, I often conform my audio (in Pro Tools) based on the waveform of the guide audio embedded in these videos. A lot of the work I've done in the last few years has all been half a frame early because of this.

Has anyone seen this before? How can I make Media Encoder output sample accurate audio without shifting?