Just had this looked at by a dealer in Fareham and had it fixed ... turns out there is a known problem with the window regulator sealing against the door chassis. It lets water in via the inner rubber seal around the door aperture. If you fold back the seal you will see that it's wet inside the seal, it runs down under the carpet from here.

Skoda must love doing this to all the models, G/F's Furby vRS has been in for the same problem!!