Hi Kazik,
Reading up on this over at the Scion forums, it appears you have a lot of company with this particular problem. The majority of posters are of the opinion that it's just the ECU adjusting itself, and thus normal behavior. Others aren't so sure, with explanations including the engine temperature sensor, mass airflow sensor, idle air control valve, coolant level, oxygen sensors and vacuum leaks. They pretty much all agree that there's no trouble codes showing. They've also mentioned the throttle body, but since you've replaced it, we can scratch that one off the list.
I'd say start with the mass airflow sensor (MAF) since it's easy to test. Just unplug it and drive the car normally. With the MAF disconnected, the car will default to preset values for the airflow based on other factors such as throttle position, so if the MAF is giving bad readings they'll go away when it's unplugged. If it stops doing the idle thing with the MAF disconnected, then it's a fair bet you should replace the airflow sensor.
Other than that, about all you can do is work your way through the list trying to eliminate as many sources of trouble as possible. If you've got access to an OBD-II scanner that can show live data, you can check the oxygen sensors while it's running, plus a lot of other things like the engine temperature.
Nothing definitive here, but hopefully you've got some things to check now and thus a place to start. Good luck; let us know what you find!
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