So... I am using a wired xbox controller.

Half the time it works ok. The other half of the time, when I press A to attack it decides that it is going to combat pause. I have unbound the combat pause option... but it keeps doing it.

The button prompts also seem to switch between a controller and a keyboard randomly.

Anyone got any clues what I am doing wrong?

Hmm, just double check your settings. I am using a ps4 controller with no issues. I had to bind all the keys before I could use it though. FYI I was using a wired xbox controller before the ps4 so it should work.

I'm also using a wired Xbox controller, but as it's a third-party transparent thing (with lights inside, etc.) I had to get the correct i.e. official driver before it would work properly.

I'll be brutally honest about the inclusion of the "controller" option in the GOG version of JE:

<rant>

To replace in-game text with instructions along the lines of "Press Button 8 to find out ..." is really freakin' lazy programming. I get they're using remapped default inputs from Windows, but this interface has sucked for years. A little compensation for this couldn't have been hard, specially since EA specially commissioned a PC port from a porting specialist...

</rant>

Sorry this isn't much of a solution.