I've only just now found that there is a Support Community for Compressor. Wish I'd known sooner.
I see my version of Compressor is 3.5.3.
I've been on a little saga.
I started out with the challenge of converting some MP4 files from a Blackberry Playbook into ProRes 422 (HQ) for editing in Final Cut. I used Compressor and the task looked fairly straight forward. I used the ProRes setting in the Compressor, converted my files and imported them into Final Cut. Video was fine but I soon found out that the audio needed rendering every time I put a clip into the Timeline. I went on-line to various chat rooms with this problem. Pretty soon a fellow was telling me that the ProRes 422 (HQ) setting in Compressor had "Audio Pass-through" as default and that this was the cause of my problem. Change it, he said, to "Linear PCM".
It took me a fair while to figure out that the ProRes setting in Compressor did not allow itself to be modified and that I'd have to create a custom preset if I was to make these changes. I set about to do that. I was able to select "QuickTime Movie" and then in "Video/Settings" choose "ProRes 422 (HQ)", in "Audio", "Linear PCM". This did solve the audio problem. Now files imported into Final Cut did not need rendering. But another problem became evident.
Whereas the ProRes 422 setting that came with Compressor in its summary page listed: "Width" and "Height" as "(100% of source)", the custom ProRes 422 (HQ) setting I'd just created has "Width" and "Height" as "320" and "240". In short the 19:9 aspect ratio of the original footage was lost. What I got both in the conversion and in Final Cut was a squished SD image.
I've played like heck with Compressor trying to see if there was some place I could get this custom version of ProRes to correspond to the aspect ratio seen in the Audio Pass-through version that came loaded in Compressor. No luck. All very mysterious.
My next step was to look to create another custom codec that would have the proper 1280 X 720 ratio. Turns out "HDV 720p 30fps" does, so now I've been converting to that. Looks fine in Final Cut - proper picture and sound.
I've been playing around a bit more and see now that I can create a custom setting using "Apple Intermediate Codec". I've tried it and it works too.
So after all this, my question: Should I be using that codec instead? Or does it really matter what codec I use for editing? Is the only real issue what codec I decide to use to output?
And while I'm at it: Does anybody have ideas why trying to create a custom setting with ProRes 422 (HQ) does not work - for my purposes at least.
I must admit this converting codecs is pretty new to me. Hopefully with time this experience will get easier and clearer.