Most of the time when I start the game, whether the controller is on before or after launch, I only get keyboard UI.

Confusingly sometimes I will get the Xbox buttons, but I can't figure it why only sometimes.

I recall that the game allows switching between gamepad and K+M on the fly. I suppose if you'll start using the gamepad the game will turn gamapad mode on?
You can also set the default controlling device in Options/Controls/Device Type. Maybe this will help.