Now it works for both MKV and FLV files. I still can't use FF~code, but as you said, I use directshowsource. Well, it works! Great!
Also, I edited code a bit to convert over-under 3D videos to anaglyph. Here it is.
video2d = AudioDub(video,audio)
video2d = ConvertToRGB32(video2d)
videoW = width(video2d)
videoH = height(video2d)
halfH = videoH / 2
f1 = Crop(video2d, 0, 0, videoW, halfH)
f2 = Crop(video2d, 0, halfH, videoW, halfH)
f1 = Lanczos4Resize(f1, videoW, videoH)
f2 = Lanczos4Resize(f2, videoW, videoH)
MergeRGB(f2.ShowRed, f1.ShowGreen, f1.ShowBlue)