I dont' have a middle schooler yet but several close friends have middle schoolers. All of them said that when their kids--confident, smart, well-adjusted kids--started middle school, they were stressed out in the early weeks by all the change: New location. First time having to be totally responsible for getting themselves to all classes on time and in the right location (in elementary, teachers led them everywhere, pretty much). Different cafeteria line to confuse them. More responsibility for lots of books and supplies. Bigger classes with unfamiliar kids. More demanding teachers. More homework. New students, new cliques, lots more social pressure than elementary school.
Your fiance's son might have some larger issue like bullying, and you need to uncover it if that's the case, but don't discount the idea that he may be reluctant to say he's just super-stressed by all the sudden change. That might be why he can't pinpoint his fears exactly. Be sure he feels secure at the school, familiar with his daily route from class to class, confident about how to use the cafeteria (is there a system new to him for paying? Does he have only a few minutes to get and eat his food, like one friend's child of mine who now has to gulp lunch after long waits in line to buy it?)
You and your fiance need to be careful that you don't let him see you fear "he will be tagged a cry baby and keep that forever" -- if he realizes you and his dad feel that way he is likely to clam up and not discuss his concerns because, well, he'll think you might consider him a bigger crybaby for being worried about "stupid stuff" like how to find his classrooms and which table to sit at during lunch. If his issues are this kind of middle-school stress and not bullying etc., he needs to be able to talk to you about it and feel his worries are legitimate. Try taking him somewhere that's quiet and he feels comfortable but is away from home -- his favorite diner or a park he really likes -- and quiz him gently about these kinds of questions. I do know one friend's daughter solved her own stress by making a map of the school that showed her classes and drawing her route on it, as well as writing out her schedule in detail and what she had to carry to each class, etc. Good luck.