I've had my IS200 about a month now (brand new). 1st and 2nd are REALLY clunky. You can feel 2nd engage as it makes the car jump/shudder.
Also the gearbox whines a lot. It actually reminds me of the 20 year old mini I used to drive. To be honest, on a car of this class (and costing this much), this really is unacceptable .
The Lexus is supposed to be equivalent to a BMW - the difference is that BMW know how to make gearboxes! (Yes, I used to own a BMW)
I am taking it back the dealer to get it sorted out(!)