Chris, I have a 300d (12 months old now) and I have not experienced any jerking or clunking from the auto transmission. I had a 250d before (MY18) and thought the box was a lot smoother than the 300d but this might be down to mileage - I have only covered 3700 miles in 12 months! The 250d covered 16000 in 18 months and was fully bedded in - if there is such a thing now a days??
I think a trip to the dealer is required - but as I'm sure you are aware with an intermittent fault/issue, they will take it for a test run and find nothing wrong! I had an issue with my drivers door window rattling (intermittently) and it took them three attempts before the door was re-aligned to resolve the issue.