Instead of using the navigate activity, use the run activity as normal. When you've got a GPS lock, hold the Up button, scroll down to Navigation, select it, scroll to Courses and select the course and select Do Course. Bingo, all your usual run fields, activity recorded as run, normal calories. I don't know why it's wrong in navigate; perhaps it assumes you're walking and uses different equations to calculate the calories, which seems odd if it's based on heart rate.