I just reread my previous posts, as I could have sworn that I mentioned it, but you are correct, I did not. I must have missed it when I lost my second post and had to retype it thanks to a power failure at my place. I apologize for unnecesarily complicating the issue because of that.
Your recap is correct. The green dots only occur with the "extend picture" option enabled, and only if it is set to 16:9. Other ratios do not invoke the problem.
However, sadly this option is also the only one that keeps the picture "in shape" as it gets horribly streched on my TV otherwise. Also, the extended picture is unlikely to be the only culprit, as there are still many files where the issue does not occur. So far, the only common denominator that I have found seems to be the ffdshow audio filter, and due to lack of time I am not entirely sure about that one either.
The only guess that makes sense to me is that either there is something wrong with the audio codec (is it possible that an audio codec distorts the image?) or that the "extend picture" option interacts with the audio codec in a way that leads to the green dots.
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