Thompson. Even for someone like me for whom English is the first and only language, this is a tricky question. "Each course" is certainly singular. but the question is what is the mood of the verb. And the tricky answer is that the verb is in the (mandative) subjuctive. Had it been in the indicative, it would have been "has", because, as you say, "each course" is singular. So Joe Offer gets an A on the grammar quiz, but many, probably most, people would make the same error the student made.