I kinda had the same problem on my golf but it wasnt unlocking any doors apart from the drivers luckily it was stil at the garage where i bought it as they had to take it to our main dealer and get them to re register the remote with the car and that sorted the problem. i hope this helps
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Common fault with VW's firstly check the door seal at the bottom and make sure it is not wet inside.
Next place is under the bonnet, just under the windscreen below the wipers you will see a long tray the "skuttle panel" leafs and muck build up in here where the drain plugs are once they get blocked the water starts coming in the car from behind the dash board. You should be able to see the problem visibly and it should be easy to clean.
I had this on a golf about 2mths ago, and a polo a while ago and also on a few passats.