Hi,
I have had experience of training a couple of dogs and handlers with this issue.
Is there a common theme to when he barks? Is it for example after you have 'gone wrong' on the course? I don't know if this applies to you but dogs who are 'faster' than their handlers often get frustrated when body language, commands and directions are not given as fast or clearly as they would like or need. As he is getting more experienced he has possibly gone up a gear in his mind and perhaps feels that you are not directing him enough - or too much!
When he barks at you, stop and stand still, and look at what your body language is doing. If you want him to do a jump on the left, is your body language facing that way? If you want him to go on ahead into a tunnel and he barks, have you commanded the tunnel verbally, and are you facing where you want him to go?
If this sounds familiar have a look at this video of my friend whose dog is very very very body driven (and a little bit frustrating too!) and see what you think.
I should add that I don't have problem with dogs that bark during a run as long as they are listening to the handler. The dog in the video loves to just bark as she runs, but she has a very definite different bark when she is frustrated with the handler - she comes and barks at her, rather than just barks while running.