Aside from all the server issues this morning, which is usually a harbinger of some incoming algorithm update, reddit also appears to have reset some user preferences.

When they first rolled out the user status feature, I went into my prefs and unchecked the box that says "allow other users to see your online status." When I logged on this morning, the green dot was back, so I went into my preferences and sure enough, the box was checked off again, as was the box that says "allow reddit to log your outgoing clicks", which I had also made sure was unchecked.