What courses should I count when calculating my GPA in major?
If no specific guidance is otherwise provided, I would include additional courses in the same department as the major. The reason for this is that anybody looking over your transcript will assume that, unless the course is clearly marked as a graduate course, it's probably a requirement for your major. 

That said, we're also not likely to check your math unless there's a gross error, and we're not likely to sweat a few hundredths of a point difference.