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