It’s highly possible that the mismatch of 30.00000 FPS from your Video Mode and the source video being 24.975025 could be causing all of the issues. In the MLT you uploaded, there are many clips where you have sped up the video clips.
The Video Mode for your project doesn’t change. It’s not variable. So for video files not of the same fps Shotcut has to adjust on the fly for each frame to the Video Mode. ~25 Frames of your source video doesn’t really equal 30 frames of the Video Mode. For each filter you apply to a video clip, Shotcut has to adjust to the Video Mode.
Have you tried to convert your video(s) to Edit-Friendly? Shotcut has a built-in conversion tool.
