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I have a '99 LS400. 55,000 miles. I have one master key. When I insert the key, there is a delay in recognition, sometimes a bit over a minute long. Dash lights up, security light flashes. Finally, it will start after the check engine light and park light turn on, and tach comes to life. There is an audible click. It always starts, eventually, with the master key.
Also, I have a copied key (ACE hardware $60) that will open the door, and will eventually be recognized, but that won't start the car.
The previous owner took it to a Lexus dealer in FL who told him to busy himself with the seatbelt until it clicked.
A local mechanic (not a dealer) said he had heard of it once, but couldn't quite remember what it was. He said it was something simple and goofy. He hooked up a computer, but was unable to find a code.