sounds like some codes should be able to be pulled up.
could be as much as a fuel pump.

Shiden Kai (Ian) might be your best source on this.  I have
an older car which flips me off from time to time, but have learned
to deal with it, UNTIL I get ambitious and disable the antitheft device.

My wife's 98 model has never given a problem.

The two systems are, fortunately or not, not exactly the same in function.

For example, the older car will not activate the starter when the antitheft
device is being petulant.  Not at all.

If the security light is flashing and your car won't start, leave your key in
the run position for 10 mins. and the security light should stop flashing.
You should then be able to start it.
My security light started coming on again about a year after paying the
dealership $450 to replace a faulty Ignition lock cylinder. I was at my wit’s
end.  My wife and kids would be stuck at night in some shopping center
parking lot waiting 10 minutes to reset the stupid thing. I was able to
Bypass, disable or Ghetto Hack my passlock II system on my 2002 Oldsmobile
Alero without relays or resistors. I  had my local Auto wiring tech install a
$5 on/off toggle switch into the yellow (resistance) wire that you are
supposed to cut and mount it under my dash in the event that a dealership
tech reset the security “fail- enable” mode or the battery stayed
disconnected for an extended period of time. All I  need to do is flip a
switch to break the circuit again while the car is running. Here is another
thread and some supporting evidence of why this actually works. The entire
job took 25 minutes. If my security light goes out, that’s when I know that
there’s a problem. You could also remove the bulb if the security light
really bothers you. This apparently works for both passlock I and passlock II.
There is an incredible link below  with high resolution pictures of the
wiring for your specific car. I included the actual photos that I used to
access my ignition lock cylinder wiring. Good luck and post with your success
stories! 12/4/05
http://www.the12volt.com/installbay/forum_posts.asp?TID=59694&PN=1&TPN=1

http://www.insurorsservicebureau.com/ISB%20technical/ISB_QA.pdf   page 4, The
PASS Key Module also has the ability to allow engine operation if it
recognizes a system fault in the ignition key reference circuit while the
engine is running. In this case the Module enters and remains in a mode which
allows the engine to be started and run without reading the resistance chip.
This mode requires that the original factory resistance chip key be in the
ignition lock
cylinder at the time the fault occurs. During this mode, the
security light will be ON all the time. When the key reference circuit is
repaired, the module will automatically reprogram itself to the mode
requiring the original resistance chip.

http://www.motorage.com/motorage/data/articlestandard/motorage/292005/169809/art
icle.pdf
page 3, If the correct key is in the cylinder and that circuit
fails while the engine is running, this is considered a
malfunction, not a theft attempt. The “Security” light
may turn on to warn of a system malfunction, but even if
it doesn’t, a key recognition circuit failure with the proper
key in the lock will cause the TDM to enter what GM
calls a “fail-enable” mode. Essentially, the theft-deterrent
system goes offline and the engine will start and run
with any key that turns the lock.

http://www.directwholesale.net/diagrams/Images.asp?ImageID=84&link=BULLDOG
http://www.directwholesale.net/diagrams/Images.asp?ImageID=87&link=BULLDOG

http://www.bulldogsecurity.com/   and click on vehicle wiring diagrams to
select your particular make.