I have a friend with a 53 plate 1.9TDi that is misfiring when at temperature. The Audi garage are baffled by it and have sent the data off to Audi in Germany.
They thought it was one of the main turbo hoses and he had it replaced at a cost of about £500 (can't remember which one now, sorry, think it was a turbo hose), they even uploaded new software (updated apparently) to the ECU which hasn't worked.
Anyone else with this problem??