This problem has been resolved for me (sort of).
Before I was placing in and out points right on the video (working with uncompressed 8-bit) in the timeline. This is what led to the blank frames. What I am doing now is making a freeze frame and placing it in my timeline. Then when I add in and out points to that and batch export, everything works properly. It’s still another step from what I was doing before, but it’s only 1 or 2 seconds of work.
Adrian – see if that works for you.