Cranks, does not start

Is the security light in the dash on? If it is not and it worked during bulb test it may not be the anti-theft.
Have you tried a second key?
What checks were done so far? Spark, fuel?

Did this truck start and run with those keys before and it just quit running?
Could you please look at the VIN number and tell me if the last six digits are lower or higher than 350000.
Nissan used two different antitheft systems on the Pathfinder in 1999.
The first of them used a standard key and a remote, the other used a chip in the key.
Your key description makes me think it is the first type.

However, reading through the information I have, if it is the security system stopping it from starting, it should not even crank regardless of the system as both state they disable the starter.

Based on the VIN and key description that vehicle has the early version of the NATS system. If triggered it shuts off power to the starter circuit and nothing else. So being as the truck does turn over but does not start it cannot be security related (unless someone altered the system or added an after-market unit)

Have the shop test for voltage at the injectors during cranking. If no voltage then check that there is power getting to the inhibitor relay and through the ECCS relay.
If there is and the ECM has good grounds Check for an actual signal coming from both cam and crankshaft sensors.

I would also test the ECCS relay on both sets of contacts. It would not take much corrosion in there to drop the voltage so the injectors will not fire.