Had the same problem when my car got re-keyed because someone stole all the keys and remotes for a bunch a cars from the valet stand in the city, but that is another story. Went to the dealership and had all the door, trunk, and ignition tumblers changed as well as got new keyless remotes. As I was pulling out of the dealership the security light started flashing. Basically the dealership did not reprogram the PCM to recognize the new keys. Remember that these cars, as do most now a days, have computer chips in the key that communicate with the on-board PCM. If the key does not have a chip, our has a chip with a different code, the PCM will not recognize it and it is not supposed to start. With a key with no chip it will not start, just turn over and die. With a key with a chip that is new or different you will experience the problem you are having. It will run sometimes, but the security light will flash, and other times it will not start or run at all. Not to say it is not a bad Anti Theft Module, but it is probably a simple reprograming of the PCM. Someone on here with more PCM tuning can probably be of more assistance in that regards? But, be careful driving it, it may finally stop starting or running and leave you dead somewhere. You probably want to have that addressed sooner rather than later if this is your daily driver. Just be careful if you have a re-programmed PCM, the dealership will down load the OEM settings and blow away anything that you may of had customazied.
