There are a couple of issues which affect the VW and Audi range which cause window problems. I asume due to platform sharing it will be the same for Skoda.
The first is the drain hole in the plenum chamber get blocked and water gets into the passenger footwell where the is a box of electrics called the convience control module which controls the alarm, elec. windows, central locking etc. When this gets wet you get some wiered stuff happening: hazzards glwoing, windows not working or working on their own etc. Check the plenum chamger for any debris and clear it out. Life the caprt in the passenger foot well and check for damp.
The other problem is the wiring in the door looms is too tight and it chaffes when the door is open, eventually rubbing through the inuslation and shorting the switches. Pull the rubber boot back between the door and car and inspect the wires.