Yes, I do think this is an issue. I am familiar with the technique, and even Shotcut includes it in Properties > menu > Extract Sub-clip…. But it creates something unreliable. It is like a miserable hacky attempt at editing, but it is provided to give people who accept the risks something. I never intended for people to use its output in a regular Shotcut editing project. After all, it is provided as an alternative to that! So, when people ask for this function, I have always recommended they try it, and if they do not like the result use Export.
Here are some things to try:
- Turn off Export > Video > Parallel processing. Maybe that accounts for a difference between preview and export.
- Use View > Resources > Convert to transcode all of the clips to an edit-friendly (intra-only) format. You should review the timing in the project afterward.
- Do an experiment using the original GoPro videos trimmed manually.
Your related post to find highlight times