If you have cuts on the timeline of a Panopto video, any captions within that trimmed area will not appear. To avoid this issue you have two options:
Option 1: Upload your videos to Panopto and cut them as you like. Save the video, download it, and then re-upload the clean, trimmed version. Then, you can apply your captions to the clean, final version. This will ensure that no captions are inside any cuts, and therefore no captions should be missing.
- OR -
Option 2: Upload your videos to Panopto and cut them as you like. Edit the captions. Save the video. In this same video, scrub through the timeline and make sure no captions begin at times that are inside of cuts. In the attached image, you can see that the end of the cut has been moved to before the 13:10 marker where the caption begins. Then apply the changes (save) again.