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Do you have any other keys to try?
Just to clarify you're saying that the engine cranks over and does not start at this time? Do both keys do the exact same thing? When it's not starting you're saying that you put the key into the ignition lock cylinder the little red security light of the key and car combination just flashes with the key in the ignition? It is designed so that when the key is inserted into the ignition that security light goes out.
Do you have the vehicle identification number available? Are you 100% certain that this has the immobilizer system? If it does the second key that you had made that seems to work in the ignition lock cylinder should need of programming. Did you have the key program so the lies are works? In your original post you said something about the security light with the key in car combination is flashing when one of the keys is used in the lock cylinder. It's very possible the original key that you had with the remote built into the key is worn out and this is why it will not work in the lock cylinder. Did you make certain that the steering wheel was not locked up against ignition cylinder? After you turned the ignition lock cylinder second key did you try and use the original key with the remote built into it to see if it then turned the lock cylinder?