In defalt atlantis only switches of one panel work - that which deals with bay doors opening. Everything else is pure cosmetics.
It is also impossible to simulate reentries with default atlatis using realistic data, but it is still nice for quick launches
Thats if I understand what you mean by "missing" right. If they are literally missing (i.e. some graphics glitch) then I'm afraid, I can't really help :-/
2 Deke: what do you mean?