I am most likely affected by the same issue: when emacs is launched to compose a git commit message, it sometimes ignores all keyboard input, but mouse input works normally. I am using Emacs 24.5.1, Ubuntu 14.04, and I3 WM.
Even more surprisingly, emacs responds to X KeyPress events sent to it through "xdotool", but not through the real keyboard. Also, "xev" indicates that emacs is receiving all KeyPress events and just dropping them internally.
After spending some time attaching GDB and stepping through code, I have found that x_filter_event() is the point in which the KeyPress event gets dropped. In a good emacs instance, event_handler_gtk receives the event and passes it on to handle_one_xevent. In a bad instance, event_handler_gdk still receives the event but never passes any KeyPress event to handle_one_xevent. In bad instances, x_filter_event always returns true for real key presses, but returns false for fake key presses from xdotool.
My best guess at this point is that the issue is something along the lines of [1]. Slowing down the system increases the likelihood of this race condition(?) happening.
To take it even further, I used xscope to intercept the emacs messages to/from X, and put a breakpoint on SYNC-Request messages. Stepping through the subsequent X messages one by one triggered the bug (1 out of 1 times) further suggesting that this is a timing issue.
I'm skipping a lot of detail here in order to keep this short. Feel free to ask me for more specifics.