Line by line interleaved 3D doesn't like interlaced content

I suppose this is obvious, but 3D screens that use line-by-line interleaved inputs for polarized output do not like interlaced content. I was having a huge problem with outputting 3D content from two interlaced video sources, and de-interlacing the source videos corrected the problem.

Here's what happens when you use interlaced sources:

... and the proper output, from progressive sources:

Full-res here:

http://echeng.com/temp/mantas-interlaced.png

http://echeng.com/temp/mantas-progressive.png

Addendum: if you tell the video it's progressive and not interlaced, it also works. This may be a Dashwood Stereo3D Toolbox plugin or Final Cut Pro issue.