Can't log in as Super Admin to one site in a MU installation

Since a few days ago, I can’t seem to log in as a Super Admin user to one specific site in a multisite install. I’ve got serveral users on that site so I did not notice right away. I’m not sure what changed exactly, probably a plugin update?

How do I debug this situation? I created a new testuser, if it has “Super Admin” set, then I can’t log in (the screen hangs and the backend PHP process terminates => eventually 502). If I uncheck, the user can log in normally. So what’s different for a Super Admin instead of a plain Admin? This doesn’t happen with other sites on the same network, nor with network administration.