Preserving original interlacing while compressing to MPEG-2 video?

One of our partner companies seems to have trouble creating interlaced MPEG-2 .m2v files using Compressor -- it always comes out progressive, no matter what options are used. Perhaps a bit of (boring) background to understand the situation:
We are a non-profit and currently negotiating with a third party to receive many hundreds of their videos for a streamable version of their video archive we're building. The originals are losslessly compressed and for some reason interlaced -- they were probably taken from Beta SP tape that way.
Our archival system would like to take MPEG-2 as "high-quality" (comparatively) input and then renders to many formats (H.264 etc.) in many containers for streaming. We do deinterlacing on those input files, if they come interlaced.
We would like to preserve this MPEG-2 file for future compression runs in future streaming formats that don't exist yet, so we think it makes sense to stay as close as possibe to the losslessly compressed original format that the third party gave us.
Can Compressor preserve the interlacing that was in the lossless source file or is this pointless? Does Compressor need to deinterlace the material anyway in order to be able to compress?
If there is no way to preserve the original interlacing and if a deinterlacing pass is part of the compression process anyway, then we'll ask for progressive material from Compressor, otherwise it would be nice to stay close to the source.
Any opinion or information is much appreciated

Thanks a lot for your response. Yes, it's 25 fps PAL video, I have one version in Apple Lossless and one in DV. So far I have tried the DV version, because I'm certain that one is interlaced. More tests with lossless follow today.
But as I understand it, most codecs today are block-based and thus would need a non-interlaced full picture to work at all? It doesn't make sense to look for blocks in material that comes in cut up bits and pieces, one half-picture per frame? So from that perspective, it would make sense for Compressor to deinterlace the source material before encoding it anyway, whether we tell it to or not.
Thanks for confirming that MPEG-2 output can be interlaced with Compressor, that's one less thing to worry about. What I'm left wondering is whether it is even mathematically possible to preserve the original interlacing through to the output MPEG-2
I'm doubting this more and more.
Probably using decent-quality deinterlacing in Compressor and making the resulting MPEG-2 progressive would do more to preserve the quality of the source material.

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http://www.megaupload.com/?d=IIKYWRXF
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I have even tried taking out every line from the new avisynth script except for the first two detailing the location of the video and audio, however this does nothing, it still crashes.
I had to convert all my original source avisynth scripts to AVI files (that are massive, as I am editing from 52 episodes of Fullmetal Alchemist: Brotherhood), and so editing the original scripts is impossible at this point, because to my knowledge, that would mean I would have to reconvert them all to AVI, which took over 16 hours, and then that would probably make me have to re-edit this entire video (which if you look at it, based on length and how much work I've put into it: is impossible, especially given the time constraints).
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These recommendations came from what I could figure out from:
http://www.animemusicvideos.org/guides/avtech31/
If anyone is curious, the song is "Libera me from Hell", and it is 44100 from what I could tell when I ran it in WINAMP (I converted it from mp3 to wav through WINAMP, if there is a better way that I am unaware of, please let me know).
I know this is extremely long, and thank you anyone who has taken their time to look through it, it is greatly appreciated.
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Dexter,
Those "black borders," if they are visible in the Program Monitor, are most likely due to a mis-match between the Source Files and the Sequence Preset.
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