Compressor choking on Motion render

Question

I've done a number of files in Motion that contain graphic elements. When I render, Compressor sometimes connects different files to the final output. Also, Compressor seems to generate a large number of timecode breaks. I think that this is happening because I render m2v files to be burned by Toast, without requiring re-encoding. Toast frequently re-encodes the m2v files until I open them in Mpeg Streamclip, fix timecode breaks and Demux them back to m2v video and ac3 audio.
Why does Compressor have this many problems? I'm using a Dual G5 2.5 machine (PowerPC)

Answer 1

I have output uncompressed video from Motion and then used Compressor to create the final m2v file. Without any explanation, 5 out of 20 of the files that Compressor produces will require re-encoding when adding them to a DVD with Toast Titanium. If I re-compress them with a lower speed setting, they will still require re-compression. Even if I set Toast to "never re-encode" it still re-encodes.
I need to understand how to prepare all files so that re-encoding is not required but I cannot find any information as to why this happens or how to prevent it. No one - even Toast people - seems to understand this.