You know your kid, but I'm with ster on this - facial expressions are not to be trusted! If your kid is able to tell you what's bothering him, NEVER discount it. schools ALWAYS tell you how wonderfully your kid is doing (in terms of adjustment). If they told you otherwise, they would have to address it, and they don't want to.
He's at the age when things start getting more abstract, and therefore often more difficult for AS kids to follow. Things are more implied and less stated, harder to follow. Your guy is not likely to know why he's having a hard time, and school is likely to discount anything that he can't back up with explanations. The only cautionary note is, if you let him have a "mental health day" (as I always call them), make sure that BEFORE you tell him he can stay home, you tell him it's just for one day, and that tomorrow he has to go to school (or whatever you plan to do). Otherwise, staying home becomes the new routine - in a big happy hurry! LOL!
Sometimes it's something about what happens first thing in the morning. Sometimes it's Mondays ... one year, my son went in to school late almost every Monday through the whole winter - the combination of Mondays, the first thing in the morning routines at school, and seasonal affective stuff wound up playing out that way. He couldn't transition from the weekend to the week smoothly, so allowing him that extra hour or two on Monday mornings made the whole rest of the week run much better. Meanwhile, you can try to figure out whether a different school program might actually be a good thing for him.
As with all kids, just knowing that you're listening to him can make a world of difference, both in how he feels, and in his willingness to share what's going on. Good luck!