Media Encoder cutting of ends of m2v files

I'm using Media Encoder to convert a bunch of .mov to MPEG2 for DVDs. On my machine, Encoder exports m2v files that are shorter than the original .mov I put in, essentially cutting off the ends of my videos. This isn't happening on my co-workers machine.
As an added note. I tried runnig the files through compressor as well. In that case, all my m2v files ended up having black video added to the end of each file.

The moral of this story:
"Don't trust QT player for evaluating final media."

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