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Problem Symptoms

WARNING: This page is about a different car, the 2002 Toyota Sequoia. However, it is still accessible from the selected car via links, so may be relevant.
Problem Symptoms

Symptom/Suspect Area Refer To
Immobilizer Is Not Set (Engine Starts With Key Codes Other Than The Registered Key Code)
ECM (1)
Engine Does Not Start
Key (2)
Wire Harness (3)
Transponder Key Coil (4)
Amplifier .....
ECM (1)
Security Indicator Is Always On
Security Indicator (5)
Wire Harness (3)
ECM (3)
Security Indicator Is Always On (Although Code Has Been Registered In The Automatic Registration Mode, Indicator Is Not Off)
Wire Harness (3)
Transponder Key Coil (4)
Amplifier .....
ECM (1)
Security Indicator Is Off (When DTC Of Immobilizer Is Output)
Wire harness (3)
Transponder Key Coil (4)
Amplifier .....
ECM (4)
Security Indicator Is Off (When DTC Of Immobilizer Is Not Output)
Wire harness (3)
ECM (1)
Security Indicator Is Abnormally Blinking
Wire Harness (3)
ECM (1)
(1) SELF-DIAGNOSTICS
(2) Check that the key which did not start the engine has been registered and that it is possible to start with other already registered keys.
(3) HOW TO TROUBLESHOOT ECU CONTROLLED SYSTEMS
(4) DTC B2798/99 COMMUNICATION MALFUNCTION NO. 2 
(5) Finish the automatic registration mode because the mode might still remain.