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Glad that you got the problem worked out. interlaced=true in the yuy2 conversion was my first thought about what might be wrong. Even if you didn't get interlaced frames with converttoyuy2() it definitely makes a difference. How big depends on the specific frames... the combination of converttoyuy2() and converttoyv12() would increase the effect.
On a side note I had some free time this week and was able to make quite a bit of progress. M-in-N decimation is working (most similar and longest string), arbitrary framerate decimation is working... post-processing for tfm is added, mainly just working on some small details atm. Probably the next release will include the decimation function, but it will only have one-pass capabilities... two pass vfr stuff I haven't gotten too yet.
In my tests the arbitrary frame rate decimation algorithm is fast, but is simply too dependent on the duplicate threshold being correctly set (both too high or too low will cause duplicates to be retained). M-in-N works much better since you can consider full cycles at a time, but is slower and still can't acheive all decimation ratios w/o having a very large N so I'm still gonna keep the other method around.
One question for anyone still reading... are single framerate methods of handling vfr content worth having? i.e. blend decimation or special field decimation for decimating 30fps progressive or 60i down to 24fps. While mkv's vfr capabilities are a much better alternative imo there are still some occasions where a single framerate or non mkv alternative might be needed.
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