Had Octavia vrs estate for about 8 months. On a few occasions we have gone to the car in the morning and all the windows are down and sunroof open. Daughter came in saying the same but said it was making a beeping noise like when you lock it. I went out and there was no noise. Any ideas

Commin enough..happened to me and it was as simple as the remote unlocking doors when pressing off an item in my pocket! So lesson learned do not have remote pressing against anything when u put the keys away.

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If you hold down the unlock button on the key fob it will lower all windows and open the sunroof. Holding the lock button closes them. Likely something was being pressed against the fob and caused this. You can turn off this feature in the settings if it becomes a problem or worries you.

I had this happen several times on a VW Jetta - most commonly all the windows would drop about 3 inches, usually on the wettest, windiest nights.  The dealer could never find anything wrong so I turned the setting off.  When I saw the Skoda had the same "convenience operation" of the windows and sunroof, I disabled it straight away.. 

I wonder if there's a way to set it so it only closes windows, because the feature can be helpful if I'm walking away and notice I left the sunroof open...