More often than not, it's an administrative choice on the part of the university for what they choose to label the program. Kind of like some schools have separate environmental engineering programs and some include them under civil.
My degree has the words "Civil Engineering" on it. The program I did was entirely structural engineering, as were all the other programs I considered. They just happened to be administratively a part of a civil engineering department.
I didn't even know there were separate structural engineering departments. "Splintering" discussion in another thread notwithstanding, I'm glad to see it.
Hg