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Why is the gearbox clunking in my '08 Volkswagen Golf?

My 2008 Volkswagen Golf (2.0FSI auto) has developed a clunk when it changes gear. This has been present for about a year, but it otherwise drives well. It has done 140,000 km. The dealer’s diagnostic tests have not detected anything both recently and when it first started. It has been recently suggested that the gearbox has been removed and inspected. Do you have any thoughts on what might be causing the clunk? Considering the cost involved it is borderline whether to proceed with the repair, but the car has otherwise performed well and given no trouble. It has been serviced regularly. Are there any other issues with this model, should I be looking for and would it be false economy to use reconditioned rather than new parts considering the substantial labour component of the repair?

It’s quite possibly caused by the clutches in the gearbox; they may need to be replaced.

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