Technical problems

My flight back to Germany is on Wednesday, so i wont actually be able to work on the video again until December, when i'm next in London. But this does at least give me plenty of time to plan what i will do. Unfortunately im having some technical problems. When i watch this video back in Reaper it looks fine- apart from the shortcomings i've identified. But now having exported it and watched it back there're black frames in between camera shots. They're in different places every time i export, but they are always somewhere to be found. It's almost as if the camera is blinking. I have no idea how to fix this, and google isn't being much help. I've double checked the frame rate i'm exporting at and it matches the frame rate my camera is filming at. I'm lost for ideas. If anyone has any i'd be glad to hear them.