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What you should do to check is change the frame rate to 29.97 in VDub and use that new source to identify if it is a problem with the frame rate or a Yua programming error.
General Format : AVI Format/Info : Audio Video Interleave File size : 143 MiB Duration : 10s 944ms Overall bit rate : 109 Mbps Video ID : 0 Format : Lagarith Codec ID : LAGS Duration : 10s 944ms Bit rate : 103 Mbps Width : 720 pixels Height : 480 pixels Display aspect ratio : 3:2 Frame rate : 59.940 fps Standard : NTSC Bits/(Pixel*Frame) : 4.992 Stream size : 135 MiB (95%) Audio ID : 1 Format : PCM Format settings, Endianness : Little Format settings, Sign : Signed Codec ID : 1 Duration : 10s 944ms Bit rate mode : Constant Bit rate : 1 536 Kbps Channel(s) : 2 channels Sampling rate : 48.0 KHz Bit depth : 16 bits Stream size : 2.00 MiB (1%) Alignment : Aligned on interleaves
General Format : AVI Format/Info : Audio Video Interleave File size : 2.75 GiB Duration : 5mn 42s Overall bit rate : 69.0 Mbps Video ID : 0 Format : Lagarith Codec ID : LAGS Duration : 5mn 41s Bit rate : 64.8 Mbps Width : 480 pixels Height : 272 pixels Display aspect ratio : 16:9 Frame rate : 59.940 fps Bits/(Pixel*Frame) : 8.274 Stream size : 2.58 GiB (94%) Audio ID : 1 Format : PCM Format settings, Endianness : Little Format settings, Sign : Signed Codec ID : 1 Duration : 5mn 42s Bit rate mode : Constant Bit rate : 1 536 Kbps Channel(s) : 2 channels Sampling rate : 48.0 KHz Bit depth : 16 bits Stream size : 62.6 MiB (2%) Alignment : Aligned on interleaves
General Complete name : Dissidia test3_IQ.mp4 Format : MPEG-4 Format profile : Base Media Codec ID : isom File size : 7.42 MiB Duration : 19s 370ms Overall bit rate mode : Variable Overall bit rate : 3 214 Kbps Encoded date : UTC 2014-11-18 20:13:56 Tagged date : UTC 2014-11-18 20:13:56 Comment : yua7 d1 f2 3d progressive 16:9 IQ Video ID : 1 Format : AVC Format/Info : Advanced Video Codec Format profile : High 4:2:2@L4.1 Format settings, CABAC : Yes Format settings, ReFrames : 4 frames Codec ID : avc1 Codec ID/Info : Advanced Video Coding Duration : 19s 252ms Source duration : 19s 278ms Bit rate : 2 911 Kbps Maximum bit rate : 5 670 Kbps Width : 480 pixels Height : 272 pixels Display aspect ratio : 16:9 Original display aspect ratio : 16:9 Frame rate mode : Variable Frame rate : 29.620 fps Minimum frame rate : 7.493 fps Maximum frame rate : 29.970 fps Color space : YUV Chroma subsampling : 4:2:2 Bit depth : 8 bits Scan type : Progressive Bits/(Pixel*Frame) : 0.753 Stream size : 6.68 MiB (90%) Source stream size : 6.68 MiB (90%) Writing library : x264 core 142 r2453 ea0ca51 Encoding settings : cabac=1 / ref=4 / deblock=1:0:0 / analyse=0x3:0x133 / me=umh / subme=10 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=24 / chroma_me=1 / trellis=2 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=6 / lookahead_threads=1 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=8 / b_pyramid=2 / b_adapt=2 / b_bias=0 / direct=3 / weightb=1 / open_gop=0 / weightp=2 / keyint=250 / keyint_min=25 / scenecut=40 / intra_refresh=0 / rc_lookahead=60 / rc=crf / mbtree=1 / crf=17.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / ip_ratio=1.40 / aq=1:1.00 Tagged date : UTC 2014-11-18 20:13:56 Audio ID : 2 Format : AAC Format/Info : Advanced Audio Codec Format profile : LC Codec ID : 40 Duration : 19s 370ms Bit rate mode : Variable Bit rate : 317 Kbps Maximum bit rate : 325 Kbps Channel(s) : 2 channels Channel positions : Front: L R Sampling rate : 48.0 KHz Compression mode : Lossy Stream size : 750 KiB (10%) Title : Ip4236a.aac@GPAC0.5.1-DEV-rev4375M Encoded date : UTC 2014-11-18 20:13:56 Tagged date : UTC 2014-11-18 20:13:56