Compressor - Output Clips Missing Frames Throughout

Compressing clips from Canon 7D (H.264) to Avid1:1x codec creates clips that are missing some frames. This results in a shorter output clip.
The missing frames are random.
The clips have a steppy playback that can be seen when stepping through the clip one frame at a time.
I am not re-timing the clips. The source is 25fps, and so is the output.
Thanks,
Ben.

G'day
Benjamin, Benjamin, Benjamin, a world of hurt today, mate.
I'm not sure this is the best workflow for you. Have you tried anything like clipwrap or Mpegstream clip to get the clips into a usable Avid format? I'm wondering if you have the correct codecs installed in the first place.
what you can do is work in smaller batches and keep sending them off in the queue.
If you have an 8 core machine you'll want to setup an render cluster, using 4 instances. Look through the manual for that in Qmaster. then when you submit, send the render batch to the cluster rather than "this machine."
I haven't been on an Avid in an age and a half, but I'd think they'd have a workflow setup for these clips, I mean rather then running off to Apple's solution.

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