OS X’s full-screen mode has had gradual improvements since its introduction a few releases ago. In Yosemite, it became more deeply entwined with Spaces and a primary “zoom” method: click the green button in a window by itself, and the app or window switches to full-screen mode. (Hold down Option to revert to the old action, which is to zoom the window to fit the display better.)
Until Mavericks, full-screen mode worked with only a single display on a Mac with other monitors, besides other quirks. Preston Hiers seems to be encountering one of these:
Going into “full-screen” mode on my apps causes my second display to go black. It just started doing this today after I did a restart. I am using a new 27-inch iMac running El Capitan. I have had my computer for over a month and never had this problem before.