I thought I had responded to the questions above back in June but I don't see my response. Logan, what I found was that if I put them in their own sequence then sent them to Color, I didn't have the problem anymore. If all else fails, see if the fit to fill function in FCP fixes it.
I had this problem once before but the frames were in the middle of the shot. In that instance, I found turning off my screen saver fixed it. Apparently every time the screen saver kicked in it was creating black frames.