I'm currently having the same issue, on the newest version (2.63) except all mouse input (motion and clicks) is disabled when a gamepad is plugged in. This has locked me into a couple of menus and kept me from starting a game because I couldn't answer whether I wanted to run the tutorial.
(Win 7 SP1 64 bit, GeForce GTX 750 Ti, driver version 451.48)
If I understand correctly, that is working as intended in 2.63. When a controller is plugged in, mouse and keyboard will be disabled and the controller will take complete priority. You can either toggle the Disable Gamepad option in Controls, or unplug the controller and it will give you control with mouse and keyboard. We will eventually make it so you can at least use the mouse to toggle options and disable the gamepad while a controller is plugged in, but for now if you don't unplug you need to navigate there with the controller to disable it while it's active.
Serious bug: inputs are broken in 2.81 when the game is started with a DirectInput controller plugged in.
The controller may not be supported (fair enough) but that leads to a weird mix where the mouse controls the cursor's position, which can hover and highlight menu items but not click, and the controller button #1 controls the clicks. Controller axes do nothing and the mouse buttons do nothing.
I did navigate the options with that combination of mouse and controller and did not find an option to disable the controller.
Then I exited the options and the continue / codex entries were overlapping for me too.
It is very unusual for a game to completely disable its keyboard support, and I would strongly recommend against it.
Thanks for the report, I'm not sure if we've tested any directinput controllers recently but I remember we tried a couple when we recently changed our input API and it was working back then. We will test it out again soon and see if there's a bug with them. Can you be more specific with what controller it was?
The game should be automatically detecting if Keyboard/Mouse was your last input and switch to it, but maybe the controller was interfering with that. If the game is restarted with the controller disconnected Keyboard/Mouse should be fine.
