Do you have any other devices? Pedals for example or is it just the joystick you have (that is being seen as two).
I needed to select every device individually under 'select controller', unbind all for each device one by one, before selcting the next device under 'select controller' then set up each one a new.
So what I mean is unbind everything, even keys if necessary, then put it all in from scratch.
(In theory, you just need to select each controller in the 'select controller' and look in current bindings to see if any has a setting for Axis Throttle, but I always liek to build my controls up in sims anyway).
There's a WOTRkeys.xca file in your appdata folders that you can also look at to see if there is another throttle listing