Pro Res PAL Interlaced - Compressor sees as progressive

This is a conundrum. I am capturing some material as ProRes PAL Standard Definition (just to save on hard drive space) and I have made a new Preset - and have gone into Advanced and ticked Interlaced and Upper Field as I know that's what the material is.
However when I then drag the completed capture to Compressor it sometimes shows as Progressive, sometimes Upper, sometimes lower
I seem to remember reading somewhere that this was Compressor "guessing" the field order and if i knew the order it would all be fine

My first impression is you're trying to make this too hard...
You have a high quality timeline which is downconverted to 1080, no problem. Once rendered, SmoothCam
should not represent a problem. If anything, SmoothCam will reduce the sudden movement that can cause problems. Any scenes where you have a high rate of change per frame (like in an explosion or a background of leaves flapping in the wind) should be marked with compression markers.
Export as a QT movie using sequence settings (include markers for DVDSP) so you have a completed source file for compression. I'm not aware of anything that will improve the quality beyond what is in the timeline, so current sequence settings are fine. Test this for playback issues.
If you are having playback problems with the sequence after export and compression, the most probable cause is excessively high bandwidth requirements. Try using the DVD: Best Quality 90 minutes preset. It generally produces a very good quality product. Any attempt to increase the quality will likely increase the bandwidth requirements that are the probable cause of the skipping.
While Sony is a big name, their DVD substrate is only mediocre. If you think the substrate is a problem, switch to Verbatim or JVC/Taiyo-Yuden.
If you are dissatisfied with the quality of the Compressor output, look into the Cinema Craft encoding products.
Hope this helps.

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    My first impression is you're trying to make this too hard...
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    If you are having playback problems with the sequence after export and compression, the most probable cause is excessively high bandwidth requirements. Try using the DVD: Best Quality 90 minutes preset. It generally produces a very good quality product. Any attempt to increase the quality will likely increase the bandwidth requirements that are the probable cause of the skipping.
    While Sony is a big name, their DVD substrate is only mediocre. If you think the substrate is a problem, switch to Verbatim or JVC/Taiyo-Yuden.
    If you are dissatisfied with the quality of the Compressor output, look into the Cinema Craft encoding products.
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