Presumably each university is free to define those programs how they wish, but I would expect a S/W engineering to focus more on the management of the software development process, and the IT to focus more on the management of enterprise-level systems.

Notice how I said "management" in both of those descriptions. A master's degree is not like a bachelor's degree - you're not learning a specific trade skill like how to program web sites or missile guidance systems. Rather, you are learning how to apply processes, business models, and conceptual frameworks to a project or business entity.

The traditional definition of IT is "business/enterprise computing" and of software engineering is "measuring and improving the productivity of creating software."