No problem. Instead of trying to handle InterruptedExceptions, you might just consider adding a volatile cancel flag that gets checked before you run each battle. That way, another thread can set the cancel flag to true when it wants RoboRunner to stop, and RoboRunner can shutdown more cleanly the next time it checks the cancel flag.
Also, to avoid possible contention over a score log, you might add some way to lock a score log (maybe add a ReentrantLock to control it that both RoboRunner and external threads can access). That way RoboJogger (or anything anyone else might write) can lock a score log when it reads it, unlock it when it's done, without worrying about stepping on RoboRunner trying to write to the score log at the same time.
Just some thoughts I had....