Jerome Colas wrote:
If I manually change it for every source file to progressive (which should be done automaticallt by Compressor), I then get a progressive output.
But that defeats Compressor's purpose and is a source for error.
I'm not sure what this means.
And I wonder whether it's a metadata thing and, and while disconcerting, whether it will have any practical effect on your project.
As a test try a single clip. Turn on frame controls with output fields set to progressive. See if it is now identified correctly. If it is bring that into FCP and compare against that against the one that is identified as interlaced.
If Frame Controls doesn't work, then I think I would use MPEG Streamclip. It's fast and has a very good batch feature.