I have the same issue with mine, had a full transmission flush and new fluid, diff oil replaced with full synthetic, just recently had KIDO tune done and although the actual shifting is much smoother than before it still has the thud (only when cold) when it shifts from 2nd - 3rd. I have done extensive searching on Google to try and find out about the cause, some say it's tune related and can be rectified by a TCM software reflash, others say it needs the TCM reset (only by a dealer supposedly) some have said that having this done rectified the issue but most said it came back once the TCM relearned. I am not overly concerned by it anymore as I have also read numerous posts that say this is normal operation and is designed to protect the transmission until the ATF warms up, I suppose it makes sense when you consider how much fluid these transmissions hold. The fact that once it's warmed up (within about a minute or so) the changes are then smooth as butter I can't see there being any other reason than it being a fail safe mechanism and part of the normal operation, especially when so many people all around the globe are experiencing the same issue