kepstin: I used smplayer and I don't think I used any custom options, not sure what deinterlacing filter is, and if I printout the pts time of output video, I see this 
pts_time=0.000000
pts_time=0.000000
pts_time=0.251053
pts_time=0.251053
pts_time=0.251054
pts_time=0.251054
pts_time=0.502106
pts_time=0.502106
pts_time=1.004213
pts_time=1.004213
pts_time=1.004213