Hey Rhune,
I have just bought Škoda Octavia 1,5 TSI 110 kW DSG e-TEC last week. I really like the car, but I can also hear a faint noise when ECO mode turns on and off. It is a quite weak sound, but beacause of the fact that the car interior is well soundproofed, it becomes a bit unpleasant. Have you got some new experiences with this issue? I assume that you also got a brand new car just recently.
I have reported this issue to the local Škoda dealer and he handed over to the manufacturer. I recomend you to do the same.
Cheers from Czech Republic!