Just took my glove box out found the said switch that clicks and you can see the body moving. Just cabled tied mine in place and hey presto….all fixed!!
So do you just need to secure the body ti fix it ? My 2014 seat ibiza toca is making the same noise! I've also noticed that starting and stopping the air recirculation button sometimes stops it. When putting the car in reverse it's starts the clicking again.
 
Hi - I have same problem - seat Ibiza toca 2015. Knocking from behind glove box when turn on / start car. Doesn’t matter if stationary or driving forward or reverse. Stops after 20 seconds or if press the recirc button myself. Starts again if switch recurve button off/ next time turn ignition on . Any idea cost to sort ? Do they need to take whole dash off or can it be accessed via glove box?
 
From reading some of the replies to this thread, I'd think that it will be worth while getting in behind the glovebox and see if you can fix the flap motor - if not you will now be in a better position to work out if you can fit a new flap motor if it comes to that.