I just exported an older project from 2.1 to 2.1.4 and opened in the terminal and input works just fine. I'm using Ubuntu Linux 16.4 64 bit and I exported with the default settings.
Does clicking the application after you've launched it from the console resolve the issue? It could be that the console is taking priority over the exported Godot game on an OS side, and that's why you can see key presses in the console and why the game isn't picking it up.
I haven't every had any problems with input related to launching from the console before, but I also haven't really used Godot 2.1.4 either... :sweat_smile: