I’m having the same issue on a Raspberry Pi with the latest Raspbian Stretch. Text works fine until either Alt key is pressed. Other key events work properly. I wasn’t sure what was causing it until I saw your post, thank you! I’ve used evtest and the keyboard diagnostics built into ioquake3 to verify that the keypresses are being acknowledged. SDL2-2.0.4 works fine, but I tested on 2.0.7 and SDL-65634e8189f0 and they both exhibit the issue. I would appreciate any suggestions as well.
Edit: Bug report created: https://bugzilla.libsdl.org/show_bug.cgi?id=4094