That's strange. As a temporary workaround, you can go to the Save folder, and create a new file called KeyBindings.lua, in which you'll have to copy the following :
KeyBindings = {
["MoveForward"] = 17,
["Jump"] = 57,
["StrafeLeft"] = 30,
["MoveBackward"] = 31,
["StrafeRight"] = 32,
}
This is the standard WSAD layout for QWERTY keyboards. If you're not comfortable with it, you can adjust the numbers above using the KeyCodes.lua file, located at the root directory of the game.
This will prevent the start screen from popping the next time you start the game.