07 Sentra 1.8s will not start consistently

ok... my car is auto tranny and has never started consistently. When I got the car it did not have the original fob so I bought a couple on ebay as per the correct FCC numbers and programmed them appropriatly. What I have to do is cycle the fob remote to lock and unlock, sometimes I have to do it more than once and then it will start. This car had minor electrical issues so I had to replace the ECM (dealer reprogrammed after installed), TCM and engine wire harness due to damage. This cleared up any minor issues accept the starting issue.

Do I have a security issue and what should I be checking? The stealer says they need to reprogram the ecm and fobs again, I call bull...