2007 Focus CL LT (australia) Transmission problem

Hi Guys,

I bought an auto 2007 LT (2008 model) with 14k kms, used by ford Australia about a 2 months ago, and soon after it developed a clunking noise when it shifts from 1st to 2nd gear (auto) . This only happens the first time it shifts after i start the engine and after that its fine. I took the car to the dealer and they said there is a problem with transmission and repaired it under warranty. The repair document states "Removed transmission to repair oil leak at front pump seal area". But my problem is it still has the clunking noise when shifting 1st to 2nd and has a slight vibration when accelerating. so I'm a bit worried. My question is Is this normal?
(They gave me a loan car until mine is repaired, same model with less kms, and it also had this noise , but had smoother shifting than mine and no vibration)

Thanks in advance
jay