The rpboblem with Compressor is that its settings are set to Automatic Field Order. When you import a Media 100 Quicktime File, it understands the field order is Lower. Try to create a new setting changing Field Order to Top, and try not to set any value under the crop settings (doing this with different values in top, left, right, bottom fields cause interlace problems). Change only crop values if you put the same values in the fields.
Hope this helps