The Climatronic on my Octavia used to click merrily away, but no faults stored on VAGCOM.
Skoda told me there was a software update that could be done, ie the climatronic ecu could be reflashed, but I never got round to getting the car in for this.
However, if you plug VAGCOM in, and open the climatronic controller, there is a setting somewhere in there (I think it may be in the drop down menu) for the flap motor relearning/repositioning. I did this on the Octavia and have had an almost silent climate control ever since.
I haven't got access to the car at the minute, but will have a look when I can. Sorry it will be on the Octavia, as my Leon only has standard air con.
Hope this helps
Mike