There is one interesting thing that I see with your source file: it uses 3:2 pull-down. That is, the frame rate of the encoded material is 24fps, but the encoding is at 29.97. In order to make up the difference, the codec (mpeg2) includes instructions to repeat some frames.
Here is the output of ffprobe (snipped out the irrelevant parts):
C:\Users\brianm\Downloads>shotcut-win64-180302\Shotcut\ffprobe.exe -show_frames -select_streams v -read_intervals “%+#4” -i "010101 Source.mkv"
Input #0, matroska,webm, from ‘010101 Source.mkv’:
Metadata:
ENCODER : Lavf57.71.100
Duration: 00:00:17.35, start: 0.167000, bitrate: 5633 kb/s
Stream #0:0: Video: mpeg2video (Main), yuv420p(tv, bottom first), 720x480 [SAR 32:27 DAR 16:9], SAR 1:1 DAR 3:2, 30.30 fps, 30.30 tbr, 1k tbn, 59.94 tbc (default)
Metadata:
DURATION : 00:00:17.350000000
Stream #0:1(eng): Audio: ac3, 48000 Hz, 5.1(side), fltp, 448 kb/s (default)
Metadata:
DURATION : 00:00:17.251000000
[FRAME]
top_field_first=0
repeat_pict=1
[/FRAME]
[FRAME]
top_field_first=1
repeat_pict=0
[FRAME]
top_field_first=1
repeat_pict=1
[/FRAME]
[FRAME]
top_field_first=0
repeat_pict=0
[/FRAME]
This cadence of alternating top_field_first and repeat_pic tells the decoder how many times to repeat each frame in order to generate the 29.97fps rate.
This is fine for players that are going to play from the beginning to the end. But it makes it more difficult to seek to a specific frame. Also, it is still a 24fps to 29.97 frame rate conversion - which is always going to feel a little bit un-smooth.
I tried the “Convert to edit friendly” option with your source file and I also still see the ocassional skip.
I also converted the file back to 24fps using an inverse telecine filter in ffmpeg:
C:\Users\brianm\Downloads>shotcut-win64-180302\Shotcut\ffmpeg.exe -i “010101 Source.mkv” -vf “fieldmatch,decimate” output.mov
That seemed to give the best results for me. But again, it is still making a bad frame rate conversion.