Can anybody wise me up on this one please.

I recently had a clutch and flywheel replaced at my local VW dealer they also replaced the rocker box cover (small oil leakage).
On collection when driving home i noticed that the engine sounds more throty and there is quite a noisy metallic knocking from the engine. I have taken it back to the dealer twice now and they say they have checked everything that they did and they cant find a problem.
It drives as normal but sounds awful any one got any ideas on what this could be i would be most interested in solving my now noisy engine.