The FR was my first machine, and after a few months (and some uneven incinerated roasts) I have developed my own way of roasting with it. I manually rotate the machine through most of the roast, and in doing so have eliminated almost all of the burned bean problem. It's not much of a hassle for me as the roasts go so quickly. Once the beans are through most of the first crack, and the beans are moving well, I put it down and let it go until it's done to my liking, usually a few snaps into the second crack.
I'm wondering if you may need to adopt a similar method?