Assuming that you are using an external gear mechanism (exbox) . . .
sd has mentioned bayonet fittings so obviously has an internal gear mech Rohloff.
Therefore it shouldn't really matter too much which gear the hub is in when disconnecting the cables.
But in this case something has gone amiss.
So, sd, disconnect the bayonet fittings and pull one hub cable all the way out until it stops, then gradually pull the other one all the way out and you should feel the 13 clicks as you go.
This will confirm that all is working ok at the hub end.
Also check your shifter rotates freely when pulling the shifter cables by hand and that the shifter rotates across the full range of 14 index numbers .
Reconnect your bayonet connectors and check again how many gears you are getting.
If its still only 13 (12 clicks), then I would guess a cable tension issue.
Try adjusting the cable tension adjusters a small amount either way and see if that sorts it.