To be fair it's not just Lexus, there's quite a few six speed gearboxes out there with this problem. I've known people with BMW M3 (manual not the SMG obviously), Madza RX-8 and Hyundai Coupe V6, all with this issue. My Hyundai Coupe had exactly the same second gear problem as my IS200, although it wasn't as bad.
I've always driven manuals but I must admit I'd go for an auto if I was going for the IS250. The tax and the better drive make it sound like a good idea.
Some Slick 50 is going in the gearbox of my IS200 at the weekend, which is known to help, so I'll report back on whether that helps :)