Hi Joshua,
I`ve the exact same problem.
I`ve posted here:
http://discussions.apple.com/thread.jspa?threadID=1780228
But despite the Mr. Kelly suspicius we didn`t figured out yet.
Did you notice that this files (that give you the quicktime -50 error) is bigger than 3GB? Because with me only happens with files bigger than 3GB!
I also notice that with old versions (of quicktime or/and proapps - compressor -) this error didn`t show up.
Try to transcode a range of files with different sizes, from 1gb to 5gb and see what happens... To me I have a trend to bigger files not transcoding because this -50 error.
Regards