Different ways to set up a WP network

I am running two different WP networks, I put one up an it was set up for my by the university tech guys for the other one. The netwiork admin dashboard looks very different in these two setups. The main thing being that the the settings menu for one offers settings for many of the plugins where as the other one offers settings for only some, very few. Why is this difference... there seems to be a fundamental difference in how each setup handles the plugins...?