octavia engine noise

hi there, i own a octavia 1.9td its on a 57 plate and done 94k miles, yesterday when i was driving a started getting a thumping noise coming i thought i had a flat got to a petrol station, all tyres correctly infalted so checked all wheel nuts all ok, the noise is still there and gets worse when you accelerate, ven if car stood still other octavia owners told me it was a common problem with the tappets, my mechanic has stripped the engine and the tappets look fine, what else can it be as he says it could be a number of things as he says the engine seems to be miss firing and when you take the oil cap of the car is breathing, it is a work car so no car means no work, all help most welcome, thanks