Audio Delayed by 1100 Samples in All Media Encoder Exports

Hello all,

Sometimes I need to add timecode overlay onto client's videos by transcoding through Media Encoder before starting audio post in pro tools. When I take a video, regardless of the source format, and export to ProRes or DNxHD it has exactly 1100 samples added to the front of the original audio once it has been processed. To say things another way, media encoder appears to be introducing 1090 samples of delay to the audio. But, and this is the important part, this is visible to me when importing into protools! When I import both the original and the re-endocded videos into, say, premier and check them: things line up just fine. But when I import into pro tools... no good, there's a consistent 1090 sample delay. However, Pro Tools doesn't see this delay with all files... only those that have been processed through media encoder into an MXF container seemingly. Like, if I re-encode from H264 Mp4 right back into H264 mp4, the audio sync is fine in pro tools. It's just the ProRes and DnxHD codecs that exhibit this behavior.

Sure, you might say that I should just cut 1090 samples off the beginning of the reference audio in pro tools each time I transcode things. And yes, that is what we do. But why is this happening in the first place?