My wife's 16 plate Fabia Monte Carlo exhibited the overheating symptoms described in this post.
I talked to the main dealer from which we bought the car and they advised that the water pump would need to be changed.
Due to the distance involved going to the main dealer, I decided to get the water pump replaced by a small local garage, who also quoted a lower price.
Unfortunately the local dealer did not suceed in fixing the problem. It turned out that they had used a compatible water pump. Further investigation then identifed that there is an solenoid fitted to the pump and it is this item that seems to cause the overheating issue. The Skoda oem replacement pump apparently comes complete with a new solenoid whilst the compatible water pump did not. The local garage were able to source a new solenoid but were only able to fit it by removing and then refitting the pump.
Its a bit 'disappointing' that the cost of the repair at the local garage turned out to significantly higher than it would have cost at the main dealer.
Hope this posting is of value to anyone else who suffers this irritating problem with the Fabia.