It might also be helpful to know more about the differences between this one course-- and everything else, past and present.
What is the subject? Is it material that he knows (too) well? Or is it completely novel material?
Does it take your son longer than peers to learn new/novel concepts? Longer to do written work? Or something else entirely?
When you say that he processes things "slowly and methodically" I'd actually call that something of a red flag with a gifted child-- it makes me think "what else is going on here?" This could really be an indication of an underlying learning disability of some kinds-- or possibly anxiety/perfectionism.
Gifted people tend to process things much FASTER (in general) than others do unless there are other things going on.
Is this particular class one in which the expectations jump is more than your son was fully prepared for (maybe a writing class, for example)? Maybe the school is hoping that the difficulties will self-correct as your DS adjusts to the new challenges of high school. I understand how frustrating that must be if you sense that there is far more going on.
What does your son think is the problem?
