[Conor Smith] “Hello all, I am having a problem when I export my master time line through compressor. I have various Motion projects in my time line that look great but after it is exported some of the layers half disappear or are totally gone. Sometimes revealing the underlying video track. The only way I have found to get around this is to make all motion projects quicktime files and then export but this is a pain in the a hole”
This implies a serious misunderstanding how things work in the FC Studio. Since you have posted in the Motion forum, I can safely infer you are trying to export the Motion timeline through Compressor and that would be improper. You should render first. Compressor really wants complete files.
Reading between the lines, you could also be implying that you are trying to export your FCP sequence via Compressor without having first rendered everything and that also would by improper. Or, at least, rather risky, as you have seen.
You do not need to make your Motion projects into QT files, you just need to render everything in your timeline BEFORE you try to process with Compressor. I hesitate to suggest exporting out of FCP using Reference because you do not seem to grasp those gotchas so export a self-contained movie from your timeline and bring that into Compressor. Do not try to Export Using Compressor. Save learning how to do that for another project.
bogiesan