I'm creating my animation on top of a clip of 4k RED footage. In the timeline, it looks perfect. Then I render it out and for just one frame, the footage is black and the animation is just sitting there on top of the black footage. Then the footage returns as normal, having skipped the last frame.
Check Frame Rates. Try rendering just the problem area to an image sequence.
Other than that we would be just guessing unless you see a lot of details about your project.