Video loops when transcoding.

I'm using Media Encoder to trans-code an orignial MKV file into a h.264 file (since it's very laggy to edit with MKV since it's so compressed).

When I try this, a weird bug/glitch happens.

For the first 10 minutes everything is fine and the trancoded video is playing back as it's supposed to. However, after around the 10 minute mark or so, the video portion loops back to the beginning while the audio portion keeps playing.

So like at minute 15, it's the audio for minute 15 but the video for minute 5. I tried both trancoding it to GoPro Cineform and h.264.

It's the same problem. I can even see it start to loop in the output preview of media encoder.

Is this a problem with my source file or a problem with Media Encoder? Is there any way to fix this?

Infact, when I was trying to recreate the problem, now it loops like the first minute of video for all 20 minutes of audio instead of even getting to 10 minutes.