Just had the 2nd service done which I mentioned the misfire and for them to replace the Skoda Auto round boot badge as showing signs of corrosion and hey presto... ECU has now been updated and no more misfire and now car seems more smoother and responsive too..!
Also they replaced the badge which is a known fault under a service bulletin.
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stevie007's post in Superb 1.8Tsi 2011 Cold Misfire was marked as the answer