Preserve color-space for keying?

[Ben_B]

I am in a bit of a pickle. I am trying to key transcoded GH1 footage and keep ending up with little line artifacts. I think Barry mentioned that this was because the original color-space of the footage was not maintained. I transcode my footage to ProRes by log and transfering in Final Cut Pro, then I remove the pulldown with compressor. In compressor there is an option to preserve the original color space when you transcode, by default it is deselected, but there is no such option in Final Cut Pro. Anyone know the best way to ingest a .MTS file (I do have the whole directory though) to ProRes (on a mac of course, there is no prores encoder for PC, although I am open to PC suggestions as well if they're free, I have a pretty kick-ass PC and I actually use it for most of my compositing, but prefer mac suggestions) while maintaining the 4:2:0 color space? Adobe Media Encoder maybe? Anyone know what I'm talking about with the line artifacts when keying (kind of like interlaced lines) and know how to deal with it? Thanks. I am trying having the "preserve source" color space option checked when I remove pulldown but I assume the Log and Transfer already converted things to 422.

Edit: Gonna play around with 5D to RGB and see what a I can get, but if you guys have any suggestions please let me know.