You may have a Theft Deterrent system problem. Refer to the item below from the Holden VR Service manual. Note that the reference to High Series BCM also applies to the other series BCMs.
1.1 THEFT DETERRENT SYSTEM - GENERAL INFORMATION
Armed
Once the theft deterrent system is enabled, it can be manually armed in one of two ways:
Actively, by pressing the button on the remote coded key (DOORS button on two button remote coded key) or,
Passively, as the High Series BCM will automatically arm 30 seconds after the ignition is turned off.
When the system is armed, the start relay (located in the engine compartment relay housing) and the engine management system ECM/PCM are disabled, preventing the engine from being started.
Disarmed
With the system disarmed, the start relay and the engine management ECM/PCM are enabled, allowing the engine to be started when the ignition switch is turned to the run position.
The theft deterrent system can be disarmed by:
Pressing the doors button on the remote coded key. This unlocks the doors, turns the interior dome lamp ON and disarms the system for 30 seconds or, until the remote coded key is inserted into the ignition switch key barrel and turned to the on or run position. This causes the High Series BCM to read a security code serial data output from the remote coded key contact pin via the remote coded key reader assembly.
The system can also be disarmed by turning the ignition switch to the ON position for approximately 45 minutes.
NOTE: Should the engine not crank when the ignition switch is turned to the START position (ie due to misaligned or a faulty remote coded key reader) then pressing the button on the remote coded key (DOORS button on two button remote coded key) will also disarm the theft deterrent system.
Theft Deterrent Alert Indicator LED
The theft deterrent alert indicator LED is used to indicate the state of the system. A flashing LED indicates that the system is armed and consequently the vehicle cannot be started. When the LED is turned off, the High Series BCM is disarmed and the engine can be started.
For vehicles with Electronic Climate Control (ECC), the theft deterrent alert indicator LED is located in the instrument facia, below the centre air outlets. If the vehicle is fitted with manual type air conditioning, the theft deterrent alert indicator LED is in the dash panel centre facia escutcheon, below the radio/cassette player.
Operation
When the ignition switch is turned to the on position, the engine management ECM/PCM will request from the High Series BCM permission to start. If the High Series BCM has received the correct security code from the remote coded key, then it will respond by enabling the start relay and giving the ECM/PCM permission to start (this allows the ECM/PCM to enable fuel system control).
If the correct security code is not detected by the High Series BCM within two seconds of the ignition being turned on, the High Series BCM will then monitor for Radio Frequency (RF) signal output from the remote coded key doors button. If the High Series BCM receives the correct RF signal output from the remote coded key, it will then enable the start relay and give the engine management ECM/PCM permission to start. This feature allows engine starting should there be a malfunction with the remote coded key reader assembly.
Should the High Series BCM not receive any communication from the engine management ECM/PCM with the ignition switched on, the High Series BCM will enable the start relay after one second delay. The engine will crank, but will not start as the engine management ECM/PCM has not enabled fuel system control (no fuel is injected).
NOTE: It is very important that the remote coded key reader is aligned correctly with the ignition lock assembly, or misalignment with the remote coded key contact may occur resulting in intermittent or no engine cranking or starting.
