OK, I tried with the ttt.264 stream and I got errors and MeGUI would not start the second pass. I tricked MeGUI by deleting the jobs from the queue and then re-enqueing the whole job, then delete just pass 1 and start pass 2.
The encode completed and the video looks fine.
So I think this is something that should be addressed by MeGUI. libavcodec is sometimes going to report harmless or recoverable errors, and MeGUI should not abort everything.
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