Might need a few more details in what you mean by "only plays the first 'scene' in each clip." When you export your sequence, and the Export Window pops up, what do you see when you scrub through the preview? Can you double-check that you are exporting the sequence and not one of the source clip files?
I have videoes that I recorded in 2k from my drone. I edited clips from the different videos and added them to a project that I used a transition to seperate. I want to export it to a MP4 so it would not be so large and I can play it from other video players such as VLC. When I do that and play it the first scene of that clip freezes on the page until the next clip and then the same happens with that clip. I've tried to reduce it in the sequence settings and it stutters when I export it