Comments in bug #34707 (now marked duplicate of bug #32457) reference this issue. Seems that another libsdl game, ppracer, can trigger the input problem.
We're dealing with two distinctly separate but seemingly related issues, both of which point fingers at gnome-screensaver.
1. (bug #32457) When using libsdl apps (and possibly others), gnome-screensaver plays dumb and can't detect activity.
2. (this bug) After deactivating gnome-screensaver, with certain apps open on screen (libsdl apps, tsclient, etc.), the inputs are locked, giving the impression of an X session freeze, which is a big deal to many users.
What we need now is to get feedback on which apps are affected by the locked input symptoms. The gnome-screensaver folks are hard to budge, so bringing lots of evidence to support the case is critical.