Something similar happened to me but more about that later.
Good news that your car is the real one.
You need to keep records/copies of all correspondence. First port of call is to approach the supplying dealer. No way they should have sold it to you and they also claim on the website/literature to carry out HPI checks on all used cars. Once you have told them the full story, tell them you want a full refund at once. Also tell VW UK so they get on the dealer's case.
It would be interesting to get the dealer to supply a copy of the HPI report they ran at the point of purchase (if they actually did it)
You might want to get a solicitor involved and see where you stand. Once you have done this, tell the dealer and VW UK to copy all correspondence to your solicitor.
Be professional and calm about it but clearly lay down what you want them to do and let them know that you're not messing about (so speak to your legal man first to know your rights).
My story........
A few years ago I bought a Fabia vRS from a well-respected indy dealer in Sheffield. The car was nearly new and they provided a HPI certificate on the car which was clean.
About a month or so later I was told (by a work colleague with access to the Experian system) that my car was tagged as 'high risk'. Someone had tagged the car after I bought it as they had an interest in it. Basically a Skoda main dealer had sold a load of stock to a local trader/dealer who had taken the cars on 30 day payment terms. This trader flogged all the cars to other traders and then did a runner before paying the main dealer for them (hence the delay in them tagging the car). Turns out the dealer I bought the car from had purchased the car in good faith.
In the end the Skoda main dealer took responsibility for the fact they had allowed themselves to get done over by a crook and they removed the bad history from the car. It was a relief but I sold the car anyway, too many bad feelings.
Anyway - hope you get it sorted chap. Best of luck.