I've never done it, but when I was reading Sherman Bell's articles regarding his testing of black powder loads he mentioned having to make some sort of cardboard shield with a small hole cut into it that he fired this loads through before they passed through the chrono. There is so much ejecta with a blackpowder load that it would cause havoc with the chronograph, like you found.
Unfortunately I don't remember any specifics such as distance to the cardboard shield or the shield's distance to the chrono, and he might not have given any.
Might be a starting spot for some experimentation though.
