Try starting D:OS EE in the keyboard UI, then in the Controls section of the Options, click the Default button, then Ok and Accept, then go back to the main menu, hit Esc to bring up the key/button prompt screen again, switch to the controller UI, and see if that makes a difference.
Try changing the controller layout used for the game in the Steam BPM options.
If you also have D:OS 2, one person with a similar problem with a DS4 controller fixed it by copying the GamePadDefinition.plist file from the the D:OS 2 app container into the app container for D:OS (after renaming the original there).
If you hold the Cmd button on game startup to get to the configuration menu, what is displayed for detected controllers in the controller section?
